1. COTAN
  2. DESCRIPTION
Browse code

Updated NEWS.md and bumped-up version

Fixed failing test

trinetra75 authored on 15/07/2025 17:06:23
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.9.4
4 
+Version: 2.9.5
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 22/06/2025 21:59:45
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DESCRIPTION
History View file @ 409891b
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.9.3
4 
+Version: 2.9.4
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 17/06/2025 12:54:06
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.9.2
4 
+Version: 2.9.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Added new clusterization methods (#115)

* Used `Seurat::RunUMAP()` as algorithm to calculate the UMAP

Used appropriate accessors on Seurat objects instead of direct access

* Fixed minor issues with call to function `Seurat::RunUMAP`

* Moved genes' section to separate function

Now genes' selection has been move to a separate function
`genesSelector()`

split clustering's UMAP plots are now outside
the Seurat clusterization function

The function `cellsUMAPPlot()` now uses the same number of features
as the clusterization

* Separated genes selection from Seurat clustering

Now in the split stage the three results of the `seuratClustering()`
function are separated:
- `genesSelection()` this function has been unified with the
already existing genes selector that was part of the function
`cellsUMAPPlot()`
- `suratClustering()` now simply returns the new clusterization and
the `PCA` used to obtain it
- The creation of the PDF output is now done directly in the
function `cellsUniformClustering()` via calls to the
function `UMAPPlot()`

Reduced the maximum point size of the `UMAPPlot()` dots

Solved a few bugs and aligned the tests to the new slightly
different output in the cluster names

* Minor improvement of the `seuratClustering()` function

* Expanded choices for `dataMethod` of the `cellsUMAPPlot() function

Added new choices: BinarizedDiscrepancy, DerivativeLogLikelihood and
SignedLogLikelihood

Added shorcuts strings for all choices

Extended calculate function `calculateLikelihoodOfObserved()` to
get a formula parameter and return all likelihood related data matrices

* Now `cellsUMAPPlot()` scales the data matrix along the genes' direction

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

Updated NEWS.md

* Preparing function `calculateReducedDataMatrix()`

* Started using new `calculateReducedDatamatrix()`

Still buggy and incomplete

* Fixed monot issue with update of pics in GitHub

* Solved issue with `calcDist()`

Fall-back using `stats::dist` was not supporting "cosine" distance
Now it uses `proxy::dist` instead.

Also restored stable PCA/clustering disrupted in previous commits

* Simplified spell-checker word list

* Added support to coex-drived dimensionality reductions

* Used new function for UMAP retriveal of data matrix

* Unified all cells' Reduction Data Matrices calculations

Now all calculations requiring to calculate PCA of cells data,
or reduction via COEX eigen-vectors, is run via the specific
function `calculateReducedDataMatrix()`

* Fixed `seuratClustering()` as was not using the passed `dataMethod`

* Fixed issue with NaN log-likelihood data matrices

* Renamed function `genesSelctor()` to `getSelectedGenes()`

Also fixed minor bug in the "HGDI" case when not enough genes
satisfy the requirement gdi >= 1.4

* Added tests about data matrices extraction

Tested `calculateLikelihoodOfObserved()`, `getDataMatrix()`
`getSelectedGenes()` and `calculateReducedDataMatrix()`

* Fixed some minor bugs left in clusterization

Fixed tests

* Updated NEWS.md

* Fixed issue with `cellsUniformClustering()`

when useCoexEigen is TRUE

* Solved spelling issues

* Fixed issue in checks about use of `requires()`

Marco Fantozzi authored on 17/06/2025 10:02:55 • GitHub committed on 17/06/2025 10:02:55
Showing 1 changed files
DESCRIPTION
History View file @ 3dd48a3
... ... 
@@ -62,9 +62,8 @@ Imports:
62 62 
     assertthat,
63 63 
     withr,
64 64 
     SingleCellExperiment,
65 
-    SummarizedExperiment,
66 
-    S4Vectors,
67 
-    proxy
65 
+    proxy,
66 
+    RSpectra
68 67 
 Suggests:
69 68 
     testthat (>= 3.2.0),
70 69 
     proto,
... ... 
@@ -84,7 +83,9 @@ Suggests:
84 83 
     qpdf,
85 84 
     GEOquery,
86 85 
     sf,
87 
-    torch
86 
+    torch,
87 
+    SummarizedExperiment,
88 
+    S4Vectors
88 89 
 Config/testthat/edition: 3
89 90 
 Language: en-US
90 91 
 biocViews:
Browse code

Solved issue with `calcDist()` (#114)

Fall-back using `stats::dist` was not supporting "cosine" distance
Now it uses `proxy::dist` instead.

Also restored stable PCA/clustering disrupted in previous commits

Marco Fantozzi authored on 05/06/2025 16:51:56 • GitHub committed on 05/06/2025 16:51:56
Showing 1 changed files
DESCRIPTION
History View file @ 7650e2a
... ... 
@@ -63,7 +63,8 @@ Imports:
63 63 
     withr,
64 64 
     SingleCellExperiment,
65 65 
     SummarizedExperiment,
66 
-    S4Vectors
66 
+    S4Vectors,
67 
+    proxy
67 68 
 Suggests:
68 69 
     testthat (>= 3.2.0),
69 70 
     proto,
Browse code

Adapted to upgraded dependencies - fixed issues (#113)

* Minimal commit to adapt to upgreded packages dependecies

Zeallot broke ... meaning, but also allowed to remove unnecessary
code check warning

* Reduced the number of 'missing binding' for variables used in ggplot

* Solved issue with changes related to function
`Seurat::as.SingleCellExperiment()`

* Fixed all `no visible binding` check results

* Fixed issue with missing `zeallot::zeallous()`

Now it checks the `zeallot` package version first

Marco Fantozzi authored on 03/06/2025 09:19:36 • GitHub committed on 03/06/2025 09:19:36
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DESCRIPTION
History View file @ f8046df
... ... 
@@ -32,19 +32,19 @@ RoxygenNote: 7.3.2
32 32 
 Roxygen: list(markdown = TRUE)
33 33 
 Imports:
34 34 
     stats,
35 
-    plyr,
36 
-    dplyr,
37 35 
     methods,
38 36 
     grDevices,
39 37 
     Matrix,
40 38 
     ggplot2,
41 39 
     ggrepel,
40 
+    gghalves,
42 41 
     ggthemes,
43 42 
     graphics,
44 43 
     parallel,
45 44 
     parallelly,
46 45 
     tibble,
47 46 
     tidyr,
47 
+    dplyr,
48 48 
     BiocSingular,
49 49 
     parallelDist,
50 50 
     ComplexHeatmap,
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 29/05/2025 14:43:28
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DESCRIPTION
History View file @ 60293c6
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.9.1
4 
+Version: 2.9.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Use umap functions from Seurat (#111)

* Used `Seurat::RunUMAP()` as algorithm to calculate the UMAP

Used appropriate accessors on Seurat objects instead of direct access

* Fixed minor issues with call to function `Seurat::RunUMAP`

* Moved genes' section to separate function

Now genes' selection has been move to a separate function
`genesSelector()`

split clustering's UMAP plots are now outside
the Seurat clusterization function

The function `cellsUMAPPlot()` now uses the same number of features
as the clusterization

* Separated genes selection from Seurat clustering

Now in the split stage the three results of the `seuratClustering()`
function are separated:
- `genesSelection()` this function has been unified with the
already existing genes selector that was part of the function
`cellsUMAPPlot()`
- `suratClustering()` now simply returns the new clusterization and
the `PCA` used to obtain it
- The creation of the PDF output is now done directly in the
function `cellsUniformClustering()` via calls to the
function `UMAPPlot()`

Reduced the maximum point size of the `UMAPPlot()` dots

Solved a few bugs and aligned the tests to the new slightly
different output in the cluster names

* Minor improvement of the `seuratClustering()` function

* Expanded choices for `dataMethod` of the `cellsUMAPPlot() function

Added new choices: BinarizedDiscrepancy, DerivativeLogLikelihood and
SignedLogLikelihood

Added shorcuts strings for all choices

Extended calculate function `calculateLikelihoodOfObserved()` to
get a formula parameter and return all likelihood related data matrices

* Now `cellsUMAPPlot()` scales the data matrix along the genes' direction

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

Updated NEWS.md

Marco Fantozzi authored on 29/05/2025 11:05:57 • GitHub committed on 29/05/2025 11:05:57
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DESCRIPTION
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... ... 
@@ -57,7 +57,6 @@ Imports:
57 57 
     Rfast,
58 58 
     stringr,
59 59 
     Seurat,
60 
-    umap,
61 60 
     dendextend,
62 61 
     zeallot,
63 62 
     assertthat,
Browse code

Updated NEWS.md and bumped-up version

Fixed documentiatio issues

trinetra75 authored on 24/04/2025 22:26:11
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DESCRIPTION
History View file @ f0f9682
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.9.0
4 
+Version: 2.9.1
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_21 branch

A Wokaty authored on 15/04/2025 16:44:54
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DESCRIPTION
History View file @ a1aa7e7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.8.0
4 
+Version: 2.9.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_21 branch

A Wokaty authored on 15/04/2025 16:44:54
Showing 1 changed files
DESCRIPTION
History View file @ 5a0ce45
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.7.5
4 
+Version: 2.8.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped-up version and updated NEWS.md

trinetra75 authored on 12/03/2025 17:10:58
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DESCRIPTION
History View file @ 2a8638a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.7.4
4 
+Version: 2.7.5
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped-up version and updated NEWS.md

trinetra75 authored on 25/02/2025 15:16:04
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DESCRIPTION
History View file @ bd5f5ce
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.7.3
4 
+Version: 2.7.4
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bugfix: use BiocSingular for PCA analysis (#101)

* Removed dependency from `PCATools` package and
thus missing `proj4` package

* Minor clean-up of integers

Marco Fantozzi authored on 25/02/2025 13:54:01 • GitHub committed on 25/02/2025 13:54:01
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DESCRIPTION
History View file @ 899f563
... ... 
@@ -46,7 +46,6 @@ Imports:
46 46 
     tibble,
47 47 
     tidyr,
48 48 
     BiocSingular,
49 
-    PCAtools,
50 49 
     parallelDist,
51 50 
     ComplexHeatmap,
52 51 
     circlize,
... ... 
@@ -65,8 +64,7 @@ Imports:
65 64 
     withr,
66 65 
     SingleCellExperiment,
67 66 
     SummarizedExperiment,
68 
-    S4Vectors,
69 
-    proj4
67 
+    S4Vectors
70 68 
 Suggests:
71 69 
     testthat (>= 3.2.0),
72 70 
     proto,
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 27/01/2025 17:01:10
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DESCRIPTION
History View file @ 5b7bd84
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.7.2
4 
+Version: 2.7.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Feature/dea contingency tables (#99)

* Added new function: clusterGeneContingencyTables()

Returns contingency tables for given gene/cluster pair

* Started writing test for the new function

* Finished tests for the new function

Marco Fantozzi authored on 27/01/2025 16:57:43 • GitHub committed on 27/01/2025 16:57:43
Showing 1 changed files
DESCRIPTION
History View file @ 613fd09
... ... 
@@ -65,7 +65,8 @@ Imports:
65 65 
     withr,
66 66 
     SingleCellExperiment,
67 67 
     SummarizedExperiment,
68 
-    S4Vectors
68 
+    S4Vectors,
69 
+    proj4
69 70 
 Suggests:
70 71 
     testthat (>= 3.2.0),
71 72 
     proto,
Browse code

Feature/alternative gene selection for split clustering (#98)

* Initial attempt

* Made possible to specify genes' selection method
in `cellsUniformClustering()`

* Updated NEWS.md and bumped-up version in DESCRIPTION

* Updated data

* Fixed test

Marco Fantozzi authored on 08/12/2024 14:50:30 • GitHub committed on 08/12/2024 14:50:30
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.7.1
4 
+Version: 2.7.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 11/11/2024 17:16:24
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DESCRIPTION
History View file @ 8b64d1c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.7.0
4 
+Version: 2.7.1
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 15:07:53
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DESCRIPTION
History View file @ 4315c6a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.6.0
4 
+Version: 2.7.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 15:07:53
Showing 1 changed files
DESCRIPTION
History View file @ 78f7c87
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.11
4 
+Version: 2.6.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 25/10/2024 17:33:53
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DESCRIPTION
History View file @ 1a9930a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.10
4 
+Version: 2.5.11
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 24/10/2024 17:47:09
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DESCRIPTION
History View file @ 56e6d4c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.9
4 
+Version: 2.5.10
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 13/10/2024 21:53:53
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DESCRIPTION
History View file @ 8588ed6
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.8
4 
+Version: 2.5.9
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped-up version

trinetra75 authored on 01/10/2024 11:53:37
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DESCRIPTION
History View file @ 2dfaa0c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.7
4 
+Version: 2.5.8
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Feature/convert to single cell experiment (#88)

* Added converters to/from SingleCellExperiment objetcs

It also supports those generated from a Seurat object

* Added tests for converters to/from SCE including those created by Seurat

Expanded ability to handle clusterizations by cell metadata title patterns

Marco Fantozzi authored on 01/10/2024 08:59:46 • GitHub committed on 01/10/2024 08:59:46
Showing 1 changed files
DESCRIPTION
History View file @ 27e1419
... ... 
@@ -62,7 +62,10 @@ Imports:
62 62 
     dendextend,
63 63 
     zeallot,
64 64 
     assertthat,
65 
-    withr
65 
+    withr,
66 
+    SingleCellExperiment,
67 
+    SummarizedExperiment,
68 
+    S4Vectors
66 69 
 Suggests:
67 70 
     testthat (>= 3.2.0),
68 71 
     proto,
Browse code

Fixed bug in `mergeUniformCellsClusters()`

Extended vignette to include current usage

trinetra75 authored on 17/09/2024 22:24:30
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DESCRIPTION
History View file @ fb24a95
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.8
4 
+Version: 2.5.7
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Feature/new ut check (#86)

* Created the new parameter classes for uniformity checks

* Setting up converters

* Solved issue with clusterization functions

It was not working properly when only 1 or 2 clusters were
the final clusterization results

Now 'saveObj = FALSE' will avoid touching the file-system
in any way: no folders and/or files creation

Bumped up automatic RoxygenNote version

* Cleaned up Roxygen decorated documentation

Added converters to list and from data.frame for checkers

* Finished preparation steps to handle Simple checks

* Replaced old style checks with new ones

Only for splitting, not merge. Still buggy.

* Fixed bugs in split usage

Validation of SimpleGDIUniformityCheck is now consistent
with expectations

Merge still not supported

* Hnadled conversion of checkers from/to dataframes

* Updated UT check functions parameters

* Minor test fix

* First changes for merge function

Fixed issue with `dfToCheckers()`

* Refactor merge function: step 2

* Re-factored using `GDICheck` class

* Restored split clusters functionality

* First step to support merge

* Solved support for merge

* Solved issues with converters to/from data.frames

Added support for more methods on `AdvancedGDIUniformityCheck`

* Fixed `liter` issues

* Spell-checker fixes

* Fixed build issues

* Full support for Advanced UT testing

Specific testing is still missing

* Fixed issues with Advance UT checks

Adjusted testers to include Advance checks

* Fixed Advanced checks bugs

* Fixed test

* Updated examples and NEWS.md, bumped up version

Marco Fantozzi authored on 15/09/2024 13:36:42 • GitHub committed on 15/09/2024 13:36:42
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.7
4 
+Version: 2.5.8
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated News.md and bumped-up version

trinetra75 authored on 04/09/2024 20:24:01
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.6
4 
+Version: 2.5.7
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Solved issue with clusterization functions (#83)

It was not working properly when only 1 or 2 clusters were
the final clusterization results

Now 'saveObj = FALSE' will avoid touching the file-system
in any way: no folders and/or files creation

Bumped up automatic RoxygenNote version

Marco Fantozzi authored on 01/09/2024 16:40:20 • GitHub committed on 01/09/2024 16:40:20
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... ... 
@@ -28,7 +28,7 @@ BugReports: https://github.com/seriph78/COTAN/issues
28 28 
 Depends: R (>= 4.3)
29 29 
 License: GPL-3
30 30 
 Encoding: UTF-8
31 
-RoxygenNote: 7.3.1
31 
+RoxygenNote: 7.3.2
32 32 
 Roxygen: list(markdown = TRUE)
33 33 
 Imports:
34 34 
     stats,
Browse code

Solved minor vignette issues (#80)

* Fixed minor issues in vignette

Now no parameters from COTAN functions will have the name `method`
as it is too confusing and can cause trouble with documentation

Fixed minor UMAP plot issue where labelled points where wrongly
plotted below the normal ones

Now default genes selection method in function `cellsUMAPPlot()`
is `HVG_Seurat`

* Fixed spelling mistakes

* Bumped-up version and updated NEWS.md

Marco Fantozzi authored on 25/06/2024 15:42:48 • GitHub committed on 25/06/2024 15:42:48
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.5
4 
+Version: 2.5.6
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bugfix/plot functions issues (#76)

* Fixed minor issues with functions: `GDIPlot()` and `clustersMarkersHeatmapPlot()`

Now parameter `groupMarkers` is optional.

* Bumped-up version and updated NEWS.md

Marco Fantozzi authored on 19/06/2024 07:30:34 • GitHub committed on 19/06/2024 07:30:34
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.4
4 
+Version: 2.5.5
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Added UMAP for cells' clusters (#75)

* Added function getProbabilityOfZero()

Returns the matrix whose components are the probability of
zero reads for given gene/cell pair...

* Added function calculateLikelihoodOfObserved()

For each gene/cell it returns the likelihood of the observed
zero/non-zero reads with repect to the modeled probability of zero

* Improved function `UMAPPLot()`

Now the function will display cluster centroids when no elements
to label are passed in

* Fixed bug in `UMAPPlot()` code

* Completed extension of function `UMAPPlot()`

Now is able to plot the clusters' names at the centroids

Now can take an array of colors for the displayed things

* Fixed bug in vignette

Now max pointSize is 3.0 instead of 5.0

* Fixed minor bugs

* Added function `cellsUMAPPlot()`

Added option to return log-normalized data

Added option to override `umap()` meta-parameters

Updated vignette

* Added more options to the `method` used by `cellsUMAPPlot()`

Added possibility to tweak a few umap hyper-parameters

* Added possibility to store/recall GDI in the COTAN object

Added support for HVG in cellsUMAPPlots() using Seurat

Updated tests/examples/documentation

* Resolved last few bugs

* Updated NEWS.md and bumped-up version

Marco Fantozzi authored on 14/06/2024 17:15:21 • GitHub committed on 14/06/2024 17:15:21
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.3
4 
+Version: 2.5.4
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and bumped up version in DESCRIPTION

trinetra75 authored on 09/06/2024 13:28:08
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DESCRIPTION
History View file @ 0afd70f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.2
4 
+Version: 2.5.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
... ... 
@@ -25,7 +25,7 @@ Description: Statistical and computational method to analyze the co-expression o
25 25 
     of gene interactions and becoming a new tool to identify cell-identity marker genes.
26 26 
 URL: https://github.com/seriph78/COTAN
27 27 
 BugReports: https://github.com/seriph78/COTAN/issues
28 
-Depends: R (>= 4.2)
28 
+Depends: R (>= 4.3)
29 29 
 License: GPL-3
30 30 
 Encoding: UTF-8
31 31 
 RoxygenNote: 7.3.1
... ... 
@@ -64,7 +64,7 @@ Imports:
64 64 
     assertthat,
65 65 
     withr
66 66 
 Suggests:
67 
-    testthat (>= 3.0.0),
67 
+    testthat (>= 3.2.0),
68 68 
     proto,
69 69 
     spelling,
70 70 
     knitr,
Browse code

Bugfix/check torch is installed (#71)

* Made `torch` support as opt-in

Now COTAN will use try to use the `torch` library only if
the option "COTAN.UseTorch" is set to `TRUE`.

This is necessary since, as of now, it is not possible to check
whether the torch installation actually ready to use without
hard failures. This might change in the future and have the feature
as opt-out instead.

* Incremented version in DESCRIPTION and updated the NEWS.md

* Updated `torch` check to avoid unwanted failures

Marco Fantozzi authored on 14/05/2024 19:55:09 • GitHub committed on 14/05/2024 19:55:09
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.1
4 
+Version: 2.5.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated NEWS.md and DESCRIPTION

Merged creation of new branch 3.19 on Bioconductor

trinetra75 authored on 01/05/2024 16:58:04
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.5.0
4 
+Version: 2.5.1
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Now it is possible to use the `torch` library for coex calculations (#67)

* Implemented faster coex evaluations via `torch` library

* Fixed issue with probabilities for negative dispersion genes

* Propagated new torch related parameters upward in the calls' chains

* Fixed issue with torch code: was using too large data type

Dropped unused cores argument from DeaOnCluster()

Aligned tests to new precision

* Added cluster' size to `checkClusterUniformity()` output

* Fixed issue with examples code

* Cleaned-up documentation for more focused man pages

* Added brief document about installing `torch`

Updated the vignette to be more in line with current COTAN usage
Running uniform clustering functions still takes 20 min,
so they are still left un-evaluated

Dropped unnecessary lines in `inst/WORDLIST`

* Lowered precision used by `torch` `cpu` devices to 32-bit floats

Fixed some spelling mistakes and non-commond wording

Marco Fantozzi authored on 20/04/2024 14:10:37 • GitHub committed on 20/04/2024 14:10:37
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DESCRIPTION
History View file @ 6aafb63
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.3.6
4 
+Version: 2.5.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
... ... 
@@ -81,7 +81,8 @@ Suggests:
81 81 
     cowplot,
82 82 
     qpdf,
83 83 
     GEOquery,
84 
-    sf
84 
+    sf,
85 
+    torch
85 86 
 Config/testthat/edition: 3
86 87 
 Language: en-US
87 88 
 biocViews:
Browse code

Better checks about handling of the clusterizations and the conditions (#61)

* Added stricted checks about Clusters with COEX and conditions

Minor refactoring

* Fixed broken example

Added News item and updated version

Marco Fantozzi authored on 09/04/2024 15:22:37 • GitHub committed on 09/04/2024 15:22:37
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.3.5
4 
+Version: 2.3.6
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bugfix/catch multi process errors (#58)

* Allowed retry on estimators functions

The functions sometimes failes due to multi-process handling
failures thus making clusterization methods unrealiable

* Now errors in mclapply() are properly propagated upward

This implies that fork failures can trigger recalculation

Marco Fantozzi authored on 31/03/2024 08:35:27 • GitHub committed on 31/03/2024 08:35:27
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.3.4
4 
+Version: 2.3.5
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bugfix/gdi speedup (#57)

* Speed-up of GDI calculations

Column sorting is now done via Rfast::colSort package

* Minor tweaking on parallel estimators

Now the minimal number of created threads can be lower than 16,
reducing the memory footprint in such cases.

* Improved logging of estimated/observed contingency tables

* Quieted the spell checker

Marco Fantozzi authored on 18/03/2024 12:23:15 • GitHub committed on 18/03/2024 12:23:15
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... ... 
@@ -28,7 +28,7 @@ BugReports: https://github.com/seriph78/COTAN/issues
28 28 
 Depends: R (>= 4.2)
29 29 
 License: GPL-3
30 30 
 Encoding: UTF-8
31 
-RoxygenNote: 7.3.0
31 
+RoxygenNote: 7.3.1
32 32 
 Roxygen: list(markdown = TRUE)
33 33 
 Imports:
34 34 
     stats,
Browse code

Bumped-up version and updated the NEWS

trinetra75 authored on 04/03/2024 18:00:57
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.3.3
4 
+Version: 2.3.4
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Feature/fix default of p value from dea (#52)

* Restored default adjustment behaviour of pValueFromDEA()

* Aligned to minor changes in `roxigen2`

Minor fix in the import of operators to align to new bug[?] in the
`roxigen2` package

* Updated News.md and DESCRIPTION to version 2.3.3

Marco Fantozzi authored on 23/01/2024 20:48:06 • GitHub committed on 23/01/2024 20:48:06
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.3.2
4 
+Version: 2.3.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
... ... 
@@ -28,7 +28,7 @@ BugReports: https://github.com/seriph78/COTAN/issues
28 28 
 Depends: R (>= 4.2)
29 29 
 License: GPL-3
30 30 
 Encoding: UTF-8
31 
-RoxygenNote: 7.2.3
31 
+RoxygenNote: 7.3.0
32 32 
 Roxygen: list(markdown = TRUE)
33 33 
 Imports:
34 34 
     stats,
Browse code

Fixed issue within the `cleanPlots()` function (#51)

* Fixed issue within the `cleanPlots()` function

When the number of cells exceeded 65536 the `hclust()` function
returns an error. Thus in such cases now COTAN does not try to find
outlayer cells (group 'B' in the plots)

* Updated news

* Fixed news

Marco Fantozzi authored on 02/01/2024 15:25:21 • GitHub committed on 02/01/2024 15:25:21
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.3.0
4 
+Version: 2.3.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Dropped all explicit uses of irlba::prcomp_irlba() (#48)

* Dropped all explicit uses of irlba::prcomp_irlba()

Using instead a more general:
PCAtools::pca(..., BSPARAM = IrlbaParam())

This also makes the package better integrated in the BioConductor
ecosystem

* Dropped all mentions of factoextra::fviz_eig()
from dependencies, documentation and vignettes

Marco Fantozzi authored on 16/11/2023 11:24:04 • GitHub committed on 16/11/2023 11:24:04
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@@ -45,7 +45,8 @@ Imports:
45 45 
     parallelly,
46 46 
     tibble,
47 47 
     tidyr,
48 
-    irlba,
48 
+    BiocSingular,
49 
+    PCAtools,
49 50 
     parallelDist,
50 51 
     ComplexHeatmap,
51 52 
     circlize,
... ... 
@@ -58,7 +59,6 @@ Imports:
58 59 
     stringr,
59 60 
     Seurat,
60 61 
     umap,
61 
-    factoextra,
62 62 
     dendextend,
63 63 
     zeallot,
64 64 
     assertthat,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 15:39:13
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.2.0
4 
+Version: 2.3.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 15:39:13
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.8
4 
+Version: 2.2.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bugfix/uniform clusterization inputs in cotan functions (#43)

* Made passing clusterizations more easy

Now all functions taking a COTAN object along a clusterization
can define the latter either by name or by value

Also used the available name to retrieve the clusters' coex when
available

* Fixed bug with picking-up coexDF

Removed unnecessary parameter in the help of UMAPPlot

* Fixed error in example

* normalizeNameAndLabels() now returns "DummyName" as name when a
clusterization but no name is given

* Increased version and updated NEWS

Marco Fantozzi authored on 27/09/2023 16:56:18 • GitHub committed on 27/09/2023 16:56:18
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.7
4 
+Version: 2.1.8
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
... ... 
@@ -80,7 +80,8 @@ Suggests:
80 80 
     BiocStyle,
81 81 
     cowplot,
82 82 
     qpdf,
83 
-    GEOquery
83 
+    GEOquery,
84 
+    sf
84 85 
 Config/testthat/edition: 3
85 86 
 Language: en-US
86 87 
 biocViews:
Browse code

Bumped-up version and updated the NEWS

trinetra75 authored on 05/07/2023 20:44:41
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.6
4 
+Version: 2.1.7
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated the NEWS and bumped-up version

trinetra75 authored on 14/06/2023 16:59:08
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DESCRIPTION
History View file @ d7e6192
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@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
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3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.5
4 
+Version: 2.1.6
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped-up version and updated NEWS

Relaxed numerical tolerance in failing tests that compare
results against stored values

trinetra75 authored on 01/06/2023 23:58:06
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DESCRIPTION
History View file @ 96c92d1
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.4
4 
+Version: 2.1.5
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped-up version and updated the NEWS

Fixed failures in tests comparing calculated against stored values
on non-Linux architectures

trinetra75 authored on 24/05/2023 09:43:12
Showing 1 changed files
DESCRIPTION
History View file @ d30d33a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.3
4 
+Version: 2.1.4
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Now using parallelDist() function (#25)

* Now using parallelDist() function

- All distance calculations done using stats::dist() are now
executed using the parallelDist::parDist() function for
improved speed

- Also moved last instance of pca calculation done using
stats::prcomp() to use irlba::prcomp_irlba() instead

- Removed the now unnecessary cosineDistance() function

* Added package parallelDist to required list

* Improved documentation about 'distance' parameter

Stated that the 'distance' parameter is now supporting all
methods from the parallelDist::parDist() function

Marco Fantozzi authored on 24/05/2023 06:32:10 • GitHub committed on 24/05/2023 06:32:10
Showing 1 changed files
DESCRIPTION
History View file @ b317b91
... ... 
@@ -46,6 +46,7 @@ Imports:
46 46 
     tibble,
47 47 
     tidyr,
48 48 
     irlba,
49 
+    parallelDist,
49 50 
     ComplexHeatmap,
50 51 
     circlize,
51 52 
     grid,
Browse code

Bumped-up version

trinetra75 authored on 16/05/2023 09:59:01
Showing 1 changed files
DESCRIPTION
History View file @ 69a6355
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.2
4 
+Version: 2.1.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped0up version and updated NEWS

trinetra75 authored on 08/05/2023 10:58:13
Showing 1 changed files
DESCRIPTION
History View file @ b0d2fdc
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.1
4 
+Version: 2.1.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped-up version

Silvia Giulia Galfre authored on 03/05/2023 16:45:37
Showing 1 changed files
DESCRIPTION
History View file @ 732f9bf
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.0
4 
+Version: 2.1.1
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 15:35:36
Showing 1 changed files
DESCRIPTION
History View file @ b56c7fc
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.0.0
4 
+Version: 2.1.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 15:35:36
Showing 1 changed files
DESCRIPTION
History View file @ 0f9d67c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 1.99.4
4 
+Version: 2.0.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Solved all documentation warnings

Bumped-up version

trinetra75 authored on 24/04/2023 17:16:55
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DESCRIPTION
History View file @ 2addc06
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 1.99.3
4 
+Version: 1.99.4
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Added pieces of the vignette V2 to V1

Bumped-up version

Reviewed README and NEWS

trinetra75 authored on 23/04/2023 15:48:17
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DESCRIPTION
History View file @ e849d8e
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 1.99.2
4 
+Version: 1.99.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped-up version

Silvia Giulia Galfre authored on 21/04/2023 11:42:31
Showing 1 changed files
DESCRIPTION
History View file @ f89419e
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 1.99.1
4 
+Version: 1.99.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Bumped up version

Silvia Giulia Galfre authored on 19/04/2023 20:29:42
Showing 1 changed files
DESCRIPTION
History View file @ 8fa35b4
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 1.99.0
4 
+Version: 1.99.1
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Updated Vignette V2

V2 vignette now uses new way to fetch data from GEO

Added GEOquery to list of suggested packages

Fixed issue with missed deletion of created files at the end
of the vignettes.

trinetra75 authored on 18/04/2023 17:01:23
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DESCRIPTION
History View file @ 5a3de70
... ... 
@@ -78,7 +78,8 @@ Suggests:
78 78 
     plotly,
79 79 
     BiocStyle,
80 80 
     cowplot,
81 
-    qpdf
81 
+    qpdf,
82 
+    GEOquery
82 83 
 Config/testthat/edition: 3
83 84 
 Language: en-US
84 85 
 biocViews:
Browse code

Improved clustersTreePlot()

New the clustersTreePlot() function returns also the COTAN object
updated with the calcualted DEAOnClusters() if it was missing

Solved dependency issue with the 'umap' package

Added example for the UMAPPlot() function

trinetra75 authored on 17/04/2023 09:47:03
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DESCRIPTION
History View file @ ac76929
... ... 
@@ -56,6 +56,7 @@ Imports:
56 56 
     Rfast,
57 57 
     stringr,
58 58 
     Seurat,
59 
+    umap,
59 60 
     factoextra,
60 61 
     dendextend,
61 62 
     zeallot,
Browse code

Version for Bioconductor rules

Silvia Giulia Galfre authored on 15/04/2023 17:13:12
Showing 1 changed files
DESCRIPTION
History View file @ 847309f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.1.0
4 
+Version: 1.99.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Fixed version number

Also minor fix in R/utilities.R

Silvia Giulia Galfre authored on 15/04/2023 17:03:17
Showing 1 changed files
DESCRIPTION
History View file @ c63793b
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 2.0.0
4 
+Version: 2.1.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Minor fix to Giuded tutorial v1 and added some missing information for authors

Silvia Giulia Galfre authored on 15/04/2023 09:49:14
Showing 1 changed files
DESCRIPTION
History View file @ de2651a
... ... 
@@ -8,7 +8,7 @@ Authors@R: c(
8 8 
   person("Fantozzi", "Marco", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-0708-5495")),
9 9 
   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
10 10 
   person("Puttini","Daniel", role = "aut", comment = c(ORCID = "0009-0006-8401-9949")),
11 
-  person("Priami","Corrado", role = "aut"),
11 
+  person("Priami","Corrado", role = "aut", comment = c(ORCID = "0000-0002-3261-6235")),
12 12 
   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
13 13 
   person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504"))
14 14 
   )
Browse code

Vignette tutorial updated (v1) The tutorial is changed with the new functions. Now it uses directly an online dataset and the old dataset was removed from the package. I also changed its name. Added Puttini and Priami as authors.

Silvia Giulia Galfre authored on 14/04/2023 13:16:19
Showing 1 changed files
DESCRIPTION
History View file @ f28af4b
... ... 
@@ -5,10 +5,13 @@ Version: 2.0.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
8 
+  person("Fantozzi", "Marco", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-0708-5495")),
8 9 
   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
10 
+  person("Puttini","Daniel", role = "aut", comment = c(ORCID = "0009-0006-8401-9949")),
11 
+  person("Priami","Corrado", role = "aut"),
9 12 
   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
10 
-  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")),
11 
-  person("Fantozzi", "Marco", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-0708-5495")) )
13 
+  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504"))
14 
+  )
12 15 
 Description: Statistical and computational method to analyze the co-expression of
13 16 
     gene pairs at single cell level. It provides the foundation for single-cell gene
14 17 
     interactome analysis. The basic idea is studying the zero UMI counts' distribution
Browse code

Addressed Warnings and Notes signalled by the BiocCheck

trinetra75 authored on 13/04/2023 21:41:50
Showing 1 changed files
DESCRIPTION
History View file @ e2ddca6
... ... 
@@ -37,6 +37,7 @@ Imports:
37 37 
     ggplot2,
38 38 
     ggrepel,
39 39 
     ggthemes,
40 
+    graphics,
40 41 
     parallel,
41 42 
     parallelly,
42 43 
     tibble,
Browse code

Updated first vignette. Updated mail in description

Silvia Giulia Galfre authored on 13/04/2023 16:33:52
Showing 1 changed files
DESCRIPTION
History View file @ 32c3749
... ... 
@@ -3,7 +3,7 @@ Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 4 
 Version: 2.0.0
5 5 
 Authors@R: c(
6 
-  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
6 
+  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
8 8 
   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
9 9 
   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
... ... 
@@ -22,7 +22,7 @@ Description: Statistical and computational method to analyze the co-expression o
22 22 
     of gene interactions and becoming a new tool to identify cell-identity marker genes.
23 23 
 URL: https://github.com/seriph78/COTAN
24 24 
 BugReports: https://github.com/seriph78/COTAN/issues
25 
-Depends: R (>= 4.1)
25 
+Depends: R (>= 4.2)
26 26 
 License: GPL-3
27 27 
 Encoding: UTF-8
28 28 
 RoxygenNote: 7.2.3
Browse code

Merged man pages for HandlingClusterizations

trinetra75 authored on 13/04/2023 12:09:41
Showing 1 changed files
DESCRIPTION
History View file @ cf2ed50
1 1 
old mode 100755
2 2 
new mode 100644
Browse code

Solved issues with broken plots due to previous commits

trinetra75 authored on 17/03/2023 18:14:14
Showing 1 changed files
DESCRIPTION
History View file @ e5fc52d
... ... 
@@ -29,7 +29,6 @@ RoxygenNote: 7.2.3
29 29 
 Roxygen: list(markdown = TRUE)
30 30 
 Imports:
31 31 
     stats,
32 
-    proto,
33 32 
     plyr,
34 33 
     dplyr,
35 34 
     methods,
... ... 
@@ -57,10 +56,10 @@ Imports:
57 56 
     dendextend,
58 57 
     zeallot,
59 58 
     assertthat,
60 
-    withr,
61 
-    qpdf
59 
+    withr
62 60 
 Suggests:
63 61 
     testthat (>= 3.0.0),
62 
+    proto,
64 63 
     spelling,
65 64 
     knitr,
66 65 
     data.table,
... ... 
@@ -73,7 +72,8 @@ Suggests:
73 72 
     Rtsne,
74 73 
     plotly,
75 74 
     BiocStyle,
76 
-    cowplot
75 
+    cowplot,
76 
+    qpdf
77 77 
 Config/testthat/edition: 3
78 78 
 Language: en-US
79 79 
 biocViews:
Browse code

Fixed issue in GDIPlot()

- Now if one of the genes groups is entirely not present in the
GDI data.frame, the code will log this occurrence and then
ignore that group instead of throwing.

- Linted files:
+ automaticCOTANObjectCreation.R
+ calculateCoex-method.R
+ cellsUniformClustering.R
+ checkClusterUniformity.R
+ clean-method.R
+ COTAN-getters.R
+ GDI-plot.R

trinetra75 authored on 28/02/2023 17:52:45
Showing 1 changed files
DESCRIPTION
History View file @ f17e6c4
... ... 
@@ -56,8 +56,9 @@ Imports:
56 56 
     factoextra,
57 57 
     dendextend,
58 58 
     zeallot,
59 
-    qpdf,
60 
-    assertthat
59 
+    assertthat,
60 
+    withr,
61 
+    qpdf
61 62 
 Suggests:
62 63 
     testthat (>= 3.0.0),
63 64 
     spelling,
Browse code

Fixed log to file

- Fixed setLoggingFile(): it was broken in case of consecutive
calls on the same file.

- Unfified handling of multi-core setup to separate function:
+ handleMultiCore()

- Aligned documentation of the output of the functions:
+ cleanPlots()
+ mergeUniformCellsClusters()

- Used lintr package to clean-up code of files:
+ utilities.R
+ AllClasses.R
+ AllGenerics.R

- Added ignored WORDLIST file for the spell_checker

trinetra75 authored on 28/02/2023 00:03:40
Showing 1 changed files
DESCRIPTION
History View file @ ec02f19
... ... 
@@ -55,7 +55,9 @@ Imports:
55 55 
     Seurat,
56 56 
     factoextra,
57 57 
     dendextend,
58 
-    zeallot
58 
+    zeallot,
59 
+    qpdf,
60 
+    assertthat
59 61 
 Suggests:
60 62 
     testthat (>= 3.0.0),
61 63 
     spelling,
Browse code

Replaced 'list[...] <-' with 'c(...) %<-%'

Replaced assignment of multiple values 'list[...] <-' from gsubfn
package with 'c(...) %<-%' from zeallot package.

It is safer, nesting and checks that the output has the right
number of elements...

trinetra75 authored on 08/01/2023 23:06:32
Showing 1 changed files
DESCRIPTION
History View file @ 1015b38
... ... 
@@ -30,7 +30,6 @@ Roxygen: list(markdown = TRUE)
30 30 
 Imports:
31 31 
     stats,
32 32 
     proto,
33 
-    gsubfn,
34 33 
     plyr,
35 34 
     dplyr,
36 35 
     methods,
... ... 
@@ -55,12 +54,14 @@ Imports:
55 54 
     stringr,
56 55 
     Seurat,
57 56 
     factoextra,
58 
-    dendextend
57 
+    dendextend,
58 
+    zeallot
59 59 
 Suggests:
60 60 
     testthat (>= 3.0.0),
61 61 
     spelling,
62 62 
     knitr,
63 63 
     data.table,
64 
+    gsubfn,
64 65 
     R.utils,
65 66 
     tidyverse,
66 67 
     rmarkdown,
Browse code

Solved issues with package building

+ Code now uses supportsMulticore() and availableCores() to avoid
asking for more cores than possible.

+ Added 'parallelly' to the list of requited packages.

+ Removed some spelling mistakes.

+ Solved issue with example code

trinetra75 authored on 29/12/2022 16:33:01
Showing 1 changed files
DESCRIPTION
History View file @ ef5588f
... ... 
@@ -40,6 +40,7 @@ Imports:
40 40 
     ggrepel,
41 41 
     ggthemes,
42 42 
     parallel,
43 
+    parallelly,
43 44 
     tibble,
44 45 
     tidyr,
45 46 
     irlba,
Browse code

Cleaned the vignette

+ Now the vignette does not throw an error on run.

+ Dropped other vignette as it was duplicated and not working.

+ Fixed some minor bugs in some plot methods.

+ Fixed bug in mechanism checking for out-of-sync coex slots.

+ Added packages to DESCRIPTION as suggested by the package check.

+ Added suggested missing imports from the same check.

trinetra75 authored on 28/12/2022 21:41:05
Showing 1 changed files
DESCRIPTION
History View file @ d96be92
... ... 
@@ -31,12 +31,14 @@ Imports:
31 31 
     stats,
32 32 
     proto,
33 33 
     gsubfn,
34 
+    plyr,
34 35 
     dplyr,
35 36 
     methods,
36 37 
     grDevices,
37 38 
     Matrix,
38 39 
     ggplot2,
39 40 
     ggrepel,
41 
+    ggthemes,
40 42 
     parallel,
41 43 
     tibble,
42 44 
     tidyr,
Browse code

Solved issue with converting old scCOTAN objects

Also dropped the cluster_homogeinity() method as no more relevant.

trinetra75 authored on 12/12/2022 16:57:44
Showing 1 changed files
DESCRIPTION
History View file @ ae8f6a0
... ... 
@@ -25,7 +25,7 @@ BugReports: https://github.com/seriph78/COTAN/issues
25 25 
 Depends: R (>= 4.1)
26 26 
 License: GPL-3
27 27 
 Encoding: UTF-8
28 
-RoxygenNote: 7.2.2
28 
+RoxygenNote: 7.2.3
29 29 
 Roxygen: list(markdown = TRUE)
30 30 
 Imports:
31 31 
     stats,
Browse code

Improved documentation

+ Added line to DESCRIPTION file to enable roxygen2 marks:
Roxygen: list(markdown = TRUE)

+ Cleaned documentation of many methods, in particular of those
already tested: that is those in AllClasses.R and utilities.R

trinetra75 authored on 05/12/2022 13:52:43
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 License: GPL-3
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 Encoding: UTF-8
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 RoxygenNote: 7.2.2
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+Roxygen: list(markdown = TRUE)
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 Imports:
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     stats,
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     proto,
Browse code

Further minor improvement of calculateCoex

Also cleaned issue with vignette calling
cell_homogeneous_clustering

trinetra75 authored on 03/12/2022 08:29:26
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@@ -7,8 +7,8 @@ Authors@R: c(
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   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
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   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
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   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
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-  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
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-  person("Fantozzi", "Marco", role = "aut")
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+  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")),
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+  person("Fantozzi", "Marco", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-0708-5495")) )
12 12 
 Description: Statistical and computational method to analyze the co-expression of
13 13 
     gene pairs at single cell level. It provides the foundation for single-cell gene
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     interactome analysis. The basic idea is studying the zero UMI counts' distribution
Browse code

Added new methods ro write clusterizations

+ New methods to manipulate the clusterizatino data:
addClusterization(), addClusterizationCoex()
and dropClusterization()

+ Fixed inconsistency in cluster names in method DEA_on_clusters:
they were inconsistent with the cluster names themselves

+ Added 'proto' as imported package for 'gsubfn'

trinetra75 authored on 28/11/2022 02:03:55
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 RoxygenNote: 7.2.2
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 Imports:
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     stats,
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+    proto,
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     gsubfn,
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     dplyr,
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     methods,
Browse code

Renamed coex to genesCoex

+ Renamed 'coex' slot to 'genesCoex', along the corresponding
accessor methods.

+ Updated DESCRIPTION with new required 'gsubfn' package.

+ Improved validation of COTAN class to include genes and cells
coex matrices.

+ Made automatic.COTAN.object.creation() into a simple function
instead of a method on a data.frame

trinetra75 authored on 23/11/2022 20:36:04
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   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
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   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
10 10 
   person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
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+  person("Fantozzi", "Marco", role = "aut")
11 12 
 Description: Statistical and computational method to analyze the co-expression of
12 13 
     gene pairs at single cell level. It provides the foundation for single-cell gene
13 14 
     interactome analysis. The basic idea is studying the zero UMI counts' distribution
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@@ -27,6 +28,7 @@ Encoding: UTF-8
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 RoxygenNote: 7.2.2
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 Imports:
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     stats,
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+    gsubfn,
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     dplyr,
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     methods,
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     grDevices,
Browse code

Refactored the clean() method

+ The clean method is now a method of the class 'COTAN' instead
of the class 'scCOTAN'.

+ Refactored and renamed fun_linear() to runEstimatesLinear().
This now uses existing estimate functions to caclualte the
required quantities.

+ Renamed function housekeepingGenes() to findHousekeepingGenes().

+ Added package 'gsubfn' to be able to assign multiple objects
returned by a function to a bunch of local variables at once.
E.G. the expression 'list[a ,b] <- c(1,3)' will define variables
'a' and 'b' and assigning them the values 1 and 3 respectively.

+ Adjusted some ggplot2 lines attributed to use 'linewidth' instead
of the now deprecated size.

+ Reshuffled COTAN methods into 3 main files in order to reduce
files cluttering:
COTAN-getters.R
COTAN-modifiers.R
COTAN-estimates.R

trinetra75 authored on 15/11/2022 16:48:11
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@@ -24,7 +24,7 @@ BugReports: https://github.com/seriph78/COTAN/issues
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 Depends: R (>= 4.1)
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 License: GPL-3
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 Encoding: UTF-8
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-RoxygenNote: 7.2.1
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+RoxygenNote: 7.2.2
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 Imports:
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     stats,
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     dplyr,
Browse code

Rebased the refactor branch on the devel one There were some conflicts: solved using as reference the last commits. This branch should become the second version of COTAN (with also the COTAN clustering).

Silvia Giulia Galfre authored on 01/11/2022 17:00:27
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1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 0.99.12
4 
+Version: 2.0.0
5 5 
 Authors@R: c(
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   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

added changes form master

putty05 authored on 16/08/2022 15:42:35 • Silvia Giulia Galfre committed on 01/11/2022 16:23:26
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@@ -24,7 +24,7 @@ BugReports: https://github.com/seriph78/COTAN/issues
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 Depends: R (>= 4.1)
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 License: GPL-3
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 Encoding: UTF-8
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-RoxygenNote: 7.2.0
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+RoxygenNote: 7.2.1
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 Imports:
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     stats,
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     dplyr,
Browse code

Removed the dependency from Python.

The PCA function used is no longer basilisk/reticulate based but uses the irlba package.
The test for PCA changed to be more robust and independent from rotations.

Added commit to removing python to the devel branch
There were some conflicts on NAMESPACE, COTAN_main, internal_functions, and in the test code.
NAMESPACE re-calculated: to do it there were problems with the library.size.plot function so I moved the GeomFlatViolin into the function geom_flat_violin.
The test files were different in the two branches: deleted both test-PCA.R and test-my-test.R and added the test for PCA into the test-COTAN_main.R

Silvia Giulia Galfre authored on 16/10/2022 10:21:09
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     parallel,
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     tibble,
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     tidyr,
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     BiocStyle,
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     cowplot
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 Config/testthat/edition: 3
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-SystemRequirements:
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-    python
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 Language: en-US
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 biocViews:
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     SystemsBiology,
Browse code

For the tests created dataset.for.test.creation(). Substituted all test data sets with the new one (test 5000 cells). Fixed a little bug in vet2mat_rfast(). Fixed a wrong call in clean(). vet2mat_rfast() was not able to rightly produce the subset matrix if the last gene was needed. When I put in clean() the part that produces also the UDE plot I used “obj” instead of “object”. Temporarly removed the get.clusters.delta.expression() and merge_cell.clusters(). In automatic.COTAN.object.creation() removed the possibility to skip mt genes. In cell_homogeneous_clustering() set the Seurat dataset creation parameters to min.cells = 1, min.features = 2. In cluster_homogeneity() removed the superfluous code for the plots (that now are directly in clean() and, for GDI, used plot_GDI() ). Removed the code to drop mt genes. Removed for now the vignette file: in progress the new one.

Silvia Giulia Galfre authored on 30/07/2022 09:24:31
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 Suggests:
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     testthat (>= 3.0.0),
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     spelling,
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-    dendextend,
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     knitr,
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Function cell_homogeneous_clustering added. In automatic.COTAN.object.creation added a parameter to NOT save the object on disk. In DEA_on_clusters added some lines to remove the unused object and clean memory.There was a problem with the functions import: one package function was overwritten by onother. The solution was using it with importFrom in the function documentation and than reconstruct the NAMESPACE file with devtools::document(). Examples for cell_homogeneous_clustering.R, cluster_homogeneity.R, cotan_on_cluster_DE.R, get.gene.clusters.R are still missing.

Silvia Giulia Galfre authored on 07/07/2022 09:02:07
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@@ -24,15 +24,15 @@ BugReports: https://github.com/seriph78/COTAN/issues
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 Depends: R (>= 4.1)
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 License: GPL-3
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 Encoding: UTF-8
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-RoxygenNote: 7.1.1
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+RoxygenNote: 7.2.0
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 Imports:
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+    stats,
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     dplyr,
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     methods,
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     grDevices,
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     Matrix,
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     ggplot2,
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     ggrepel,
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-    stats,
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     parallel,
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     tibble,
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     tidyr,
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     utils,
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     rlang,
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     Rfast,
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+    stringr,
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     Seurat,
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-    dendextend,
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+    factoextra,
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+    dendextend
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 Suggests:
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     testthat (>= 3.0.0),
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     knitr,
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     rmarkdown,
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     htmlwidgets,
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 Config/testthat/edition: 3
Browse code

DEA on cluster, cluster homogeneity, cosine dissimilarity, get gene clusters added the functions. Added some line in main for back compatibility. Changed GDI plot function for automatically use the right number of colors.

seriph78 authored on 13/06/2022 17:22:48
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     circlize,
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     grid,
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     scales,
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+    RColorBrewer,
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     rlang,
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 Suggests:
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     testthat (>= 3.0.0),
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Ready for push to Bioconductor. Back compatibility for coex matrix added. Removed some warning and notes from checks (both Bioconductor and R). Specific files for est.min.parameters, get.gene.coexpression.space and extract.coex functions

seriph78 authored on 29/03/2022 10:40:01
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     tidyr,
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     GeneExpression,
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     SingleCell
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 VignetteBuilder: knitr
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+LazyData: false
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COEX estimation faster and specific files for get.pval and get.GDI. Create specific file for functions get.pval and get.GDI. These two functions are also corrected for the new COEX storage. Changed the COEX estimation using only one observed matrix (instead of 4). Documenation for the two function vec2mat and mat2vec crated. New tests and test dataset checked and fixed. Plot_heatmap fixed. Change version 0.99.12

seriph78 authored on 24/03/2022 10:13:14
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 Package: COTAN
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 Type: Package
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 Title: COexpression Tables ANalysis
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-Version: 0.99.11
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+Version: 0.99.12
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 Authors@R: c(
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   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
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   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
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     grid,
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     scales,
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     utils,
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-    rlang
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+    rlang,
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+    Rfast
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 Suggests:
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     testthat (>= 3.0.0),
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     spelling,
Browse code

Functions split started. We started to split function in different files. Some minor correction on automatic cotan structure creation (specially to improve the runability and make it lighter on RAM usage)

seriph78 authored on 19/01/2022 17:18:14
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     stats,
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     parallel,
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     tibble,
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+    Seurat,
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     tidyr,
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     basilisk,
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     reticulate,
Browse code

Added cluster_homogeneity, cotan_on_cluster_DE and get.subset

Silvia Giulia Galfre authored on 26/12/2021 17:29:58 • seriph78 committed on 28/12/2021 17:44:08
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-Version: 0.99.10
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 Authors@R: c(
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   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
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   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
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   person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
11 11 
 Description: Statistical and computational method to analyze the co-expression of
12 12 
     gene pairs at single cell level. It provides the foundation for single-cell gene
13 
-    interactome analysis. The basic idea is studying the zero UMI counts’ distribution
13 
+    interactome analysis. The basic idea is studying the zero UMI counts' distribution
14 14 
     instead of focusing on positive counts; this is done with a generalized contingency
15 15 
     tables framework. COTAN can effectively assess the correlated or anti-correlated
16 16 
     expression of gene pairs. It provides a numerical index related to the correlation and an
Browse code

Fixed vignette and some notes. Add the quotes suggested by github issue #1. Removed \dontrun. Substituted “=” with <- . In the guided_tutorial it is added the header and used the BiocStyle.

seriph78 authored on 26/12/2021 09:55:08
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   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
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   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
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     Rtsne,
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     plotly,
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     dendextend,
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 Config/testthat/edition: 3
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Updated version to commit on Bioconductor

seriph78 authored on 11/08/2021 09:24:06
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   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
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   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Problem with the vignette html fixed. There was a function returning the object that was not assigned to the object itself. Version updated.

seriph78 authored on 18/07/2021 19:48:26
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   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
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Added functions to avoid the use of @ in examples and vignette. Functions: add.row.to.metadata, drop.genes.cells, get.a,get.cell.number, get.cell.size, get.constitutive.genes, get.genes, get.lambda, get.metadata, get.normdata, get.nu, get.rawdata. Changed al control loops with “stop.if.not”. Changed all ranges “1:something” with seq_len() and seq_along(). Version number updated.

seriph78 authored on 18/07/2021 14:00:04
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Configure warning Changed the permission to execute the configure files.

seriph78 authored on 04/07/2021 15:17:34
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Win32 not supported. We added a .BBSoption file as suggested to explicitly tell that win32 is not supported (for the use of basilisk package)

seriph78 authored on 04/07/2021 15:00:39
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-  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
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-  person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
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-  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
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-  person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
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-  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
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-Description: Statistical and computational method to analyze the co-expression of
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-    gene pairs at single cell level. It provides the foundation for single-cell gene
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-    interactome analysis. The basic idea is studying the zero UMI counts’ distribution
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-    instead of focusing on positive counts; this is done with a generalized contingency
15 
-    tables framework. COTAN can effectively assess the correlated or anti-correlated
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-    expression of gene pairs. It provides a numerical index related to the correlation and an
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-    approximate p-value for the associated independence test. COTAN can also evaluate whether
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-    single genes are differentially expressed, scoring them with a newly defined global
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-    differentiation index. Moreover, this approach provides ways to plot and cluster genes
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-    according to their co-expression pattern with other genes, effectively helping the study
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-    of gene interactions and becoming a new tool to identify cell-identity marker genes.
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-URL: https://github.com/seriph78/COTAN
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-BugReports: https://github.com/seriph78/COTAN/issues
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-Depends: R (>= 4.1)
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-License: GPL-3
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-Encoding: UTF-8
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-RoxygenNote: 7.1.1
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-Imports:
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-    dplyr,
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-    methods,
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-    grDevices,
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-    Matrix,
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-    ggplot2,
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-    ggrepel,
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-    stats,
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-    parallel,
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-    tibble,
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-    tidyr,
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-    basilisk,
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-    reticulate,
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-    ComplexHeatmap,
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-    circlize,
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-    grid,
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-    scales,
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-    utils,
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-    rlang
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-Suggests:
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-    knitr,
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-    data.table,
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-    R.utils,
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-    tidyverse,
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-    rmarkdown,
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-    htmlwidgets,
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-    MASS,
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-    factoextra,
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-    Rtsne,
59 
-    plotly,
60 
-    dendextend,
61 
-    cowplot
62 
-Config/testthat/edition: 3
63 
-SystemRequirements:
64 
-    python
65 
-Language: en-US
66 
-biocViews:
67 
-    SystemsBiology,
68 
-    Transcriptomics,
69 
-    GeneExpression,
70 
-    SingleCell
71 
-VignetteBuilder: knitr
1 
+Package: COTAN
2 
+Type: Package
3 
+Title: COexpression Tables ANalysis
4 
+Version: 0.99.5
5 
+Authors@R: c(
6 
+  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 
+  person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
8 
+  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
9 
+  person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
10 
+  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
11 
+Description: Statistical and computational method to analyze the co-expression of
12 
+    gene pairs at single cell level. It provides the foundation for single-cell gene
13 
+    interactome analysis. The basic idea is studying the zero UMI counts’ distribution
14 
+    instead of focusing on positive counts; this is done with a generalized contingency
15 
+    tables framework. COTAN can effectively assess the correlated or anti-correlated
16 
+    expression of gene pairs. It provides a numerical index related to the correlation and an
17 
+    approximate p-value for the associated independence test. COTAN can also evaluate whether
18 
+    single genes are differentially expressed, scoring them with a newly defined global
19 
+    differentiation index. Moreover, this approach provides ways to plot and cluster genes
20 
+    according to their co-expression pattern with other genes, effectively helping the study
21 
+    of gene interactions and becoming a new tool to identify cell-identity marker genes.
22 
+URL: https://github.com/seriph78/COTAN
23 
+BugReports: https://github.com/seriph78/COTAN/issues
24 
+Depends: R (>= 4.1)
25 
+License: GPL-3
26 
+Encoding: UTF-8
27 
+RoxygenNote: 7.1.1
28 
+Imports:
29 
+    dplyr,
30 
+    methods,
31 
+    grDevices,
32 
+    Matrix,
33 
+    ggplot2,
34 
+    ggrepel,
35 
+    stats,
36 
+    parallel,
37 
+    tibble,
38 
+    tidyr,
39 
+    basilisk,
40 
+    reticulate,
41 
+    ComplexHeatmap,
42 
+    circlize,
43 
+    grid,
44 
+    scales,
45 
+    utils,
46 
+    rlang
47 
+Suggests:
48 
+    testthat (>= 3.0.0),
49 
+    spelling,
50 
+    knitr,
51 
+    data.table,
52 
+    R.utils,
53 
+    tidyverse,
54 
+    rmarkdown,
55 
+    htmlwidgets,
56 
+    MASS,
57 
+    factoextra,
58 
+    Rtsne,
59 
+    plotly,
60 
+    dendextend,
61 
+    cowplot
62 
+Config/testthat/edition: 3
63 
+SystemRequirements:
64 
+    python
65 
+Language: en-US
66 
+biocViews:
67 
+    SystemsBiology,
68 
+    Transcriptomics,
69 
+    GeneExpression,
70 
+    SingleCell
71 
+VignetteBuilder: knitr
Browse code

Check for Windows We added a control to check if the program is running on a windows machine and in this case, the core number used is set to 1.

seriph78 authored on 27/06/2021 09:28:47
Showing 1 changed files
DESCRIPTION
History View file @ 4dc2955
... ... 
@@ -1,71 +1,71 @@
1 
-Package: COTAN
2 
-Type: Package
3 
-Title: COexpression Tables ANalysis
4 
-Version: 0.99.3
5 
-Authors@R: c(
6 
-  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 
-  person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
8 
-  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
9 
-  person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
10 
-  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
11 
-Description: Statistical and computational method to analyze the co-expression of
12 
-    gene pairs at single cell level. It provides the foundation for single-cell gene
13 
-    interactome analysis. The basic idea is studying the zero UMI counts’ distribution
14 
-    instead of focusing on positive counts; this is done with a generalized contingency
15 
-    tables framework. COTAN can effectively assess the correlated or anti-correlated
16 
-    expression of gene pairs. It provides a numerical index related to the correlation and an
17 
-    approximate p-value for the associated independence test. COTAN can also evaluate whether
18 
-    single genes are differentially expressed, scoring them with a newly defined global
19 
-    differentiation index. Moreover, this approach provides ways to plot and cluster genes
20 
-    according to their co-expression pattern with other genes, effectively helping the study
21 
-    of gene interactions and becoming a new tool to identify cell-identity marker genes.
22 
-URL: https://github.com/seriph78/COTAN
23 
-BugReports: https://github.com/seriph78/COTAN/issues
24 
-Depends: R (>= 4.1)
25 
-License: GPL-3
26 
-Encoding: UTF-8
27 
-RoxygenNote: 7.1.1
28 
-Imports:
29 
-    dplyr,
30 
-    methods,
31 
-    grDevices,
32 
-    Matrix,
33 
-    ggplot2,
34 
-    ggrepel,
35 
-    stats,
36 
-    parallel,
37 
-    tibble,
38 
-    tidyr,
39 
-    basilisk,
40 
-    reticulate,
41 
-    ComplexHeatmap,
42 
-    circlize,
43 
-    grid,
44 
-    scales,
45 
-    utils,
46 
-    rlang
47 
-Suggests:
48 
-    testthat (>= 3.0.0),
49 
-    spelling,
50 
-    knitr,
51 
-    data.table,
52 
-    rmarkdown,
53 
-    R.utils,
54 
-    tidyverse,
55 
-    htmlwidgets,
56 
-    MASS,
57 
-    factoextra,
58 
-    Rtsne,
59 
-    plotly,
60 
-    dendextend,
61 
-    cowplot
62 
-Config/testthat/edition: 3
63 
-SystemRequirements:
64 
-    python
65 
-Language: en-US
66 
-biocViews:
67 
-    SystemsBiology,
68 
-    Transcriptomics,
69 
-    GeneExpression,
70 
-    SingleCell
71 
-VignetteBuilder: knitr
1 
+Package: COTAN
2 
+Type: Package
3 
+Title: COexpression Tables ANalysis
4 
+Version: 0.99.4
5 
+Authors@R: c(
6 
+  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 
+  person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
8 
+  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
9 
+  person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
10 
+  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
11 
+Description: Statistical and computational method to analyze the co-expression of
12 
+    gene pairs at single cell level. It provides the foundation for single-cell gene
13 
+    interactome analysis. The basic idea is studying the zero UMI counts’ distribution
14 
+    instead of focusing on positive counts; this is done with a generalized contingency
15 
+    tables framework. COTAN can effectively assess the correlated or anti-correlated
16 
+    expression of gene pairs. It provides a numerical index related to the correlation and an
17 
+    approximate p-value for the associated independence test. COTAN can also evaluate whether
18 
+    single genes are differentially expressed, scoring them with a newly defined global
19 
+    differentiation index. Moreover, this approach provides ways to plot and cluster genes
20 
+    according to their co-expression pattern with other genes, effectively helping the study
21 
+    of gene interactions and becoming a new tool to identify cell-identity marker genes.
22 
+URL: https://github.com/seriph78/COTAN
23 
+BugReports: https://github.com/seriph78/COTAN/issues
24 
+Depends: R (>= 4.1)
25 
+License: GPL-3
26 
+Encoding: UTF-8
27 
+RoxygenNote: 7.1.1
28 
+Imports:
29 
+    dplyr,
30 
+    methods,
31 
+    grDevices,
32 
+    Matrix,
33 
+    ggplot2,
34 
+    ggrepel,
35 
+    stats,
36 
+    parallel,
37 
+    tibble,
38 
+    tidyr,
39 
+    basilisk,
40 
+    reticulate,
41 
+    ComplexHeatmap,
42 
+    circlize,
43 
+    grid,
44 
+    scales,
45 
+    utils,
46 
+    rlang
47 
+Suggests:
48 
+    testthat (>= 3.0.0),
49 
+    spelling,
50 
+    knitr,
51 
+    data.table,
52 
+    R.utils,
53 
+    tidyverse,
54 
+    rmarkdown,
55 
+    htmlwidgets,
56 
+    MASS,
57 
+    factoextra,
58 
+    Rtsne,
59 
+    plotly,
60 
+    dendextend,
61 
+    cowplot
62 
+Config/testthat/edition: 3
63 
+SystemRequirements:
64 
+    python
65 
+Language: en-US
66 
+biocViews:
67 
+    SystemsBiology,
68 
+    Transcriptomics,
69 
+    GeneExpression,
70 
+    SingleCell
71 
+VignetteBuilder: knitr
Browse code

Forget again to change the version.

seriph78 authored on 21/06/2021 09:19:40
Showing 1 changed files
DESCRIPTION
History View file @ 51f98b7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 0.99.2
4 
+Version: 0.99.3
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Forgotten to change the version number.

seriph78 authored on 21/06/2021 08:08:14
Showing 1 changed files
DESCRIPTION
History View file @ dabf489
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 0.99.1
4 
+Version: 0.99.2
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Previous version gave WARNING “checking data for ASCII and uncompressed saves”. It should be solved re-saving all test files with save([file],file="[name].RDS", compress='xz')

seriph78 authored on 20/06/2021 14:53:08
Showing 1 changed files
DESCRIPTION
History View file @ 70c9b22
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 0.99.0
4 
+Version: 0.99.1
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Changed version for Bioconductor first submission.

seriph78 authored on 12/06/2021 13:55:17
Showing 1 changed files
DESCRIPTION
History View file @ 5fad94b
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 0.1.1
4 
+Version: 0.99.0
5 5 
 Authors@R: c(
6 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
7 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
Browse code

Smaller size. Some dataset used for examples and tests were changed to make the package smaller. In particular, some datasets used for the examples are now used also for tests and are no longer duplicated in the test directory. All TRUE and FALSE are now corrected (not shorter version).

seriph78 authored on 12/06/2021 13:32:00
Showing 1 changed files
DESCRIPTION
History View file @ d5943d9
... ... 
@@ -21,7 +21,7 @@ Description: Statistical and computational method to analyze the co-expression o
21 21 
     of gene interactions and becoming a new tool to identify cell-identity marker genes.
22 22 
 URL: https://github.com/seriph78/COTAN
23 23 
 BugReports: https://github.com/seriph78/COTAN/issues
24 
-Depends: R (>= 4.0)
24 
+Depends: R (>= 4.1)
25 25 
 License: GPL-3
26 26 
 Encoding: UTF-8
27 27 
 RoxygenNote: 7.1.1
... ... 
@@ -69,4 +69,3 @@ biocViews:
69 69 
     GeneExpression,
70 70 
     SingleCell
71 71 
 VignetteBuilder: knitr
72 
-LazyData: true
Browse code

Changed to upload to Bioconductor.

To follow the Bioconductor istructions some more examples were added.
Also part of the DESCRIPRION was changed.
- R CMD check succeeded
- BiocCheck passed with two warning
- it does not pass the BiocCheckGitClone: "System Files found that should
not be git tracked" also if the files are in gitignore.

seriph78 authored on 20/05/2021 16:16:33
Showing 1 changed files
DESCRIPTION
History View file @ b09f796
... ... 
@@ -1,16 +1,14 @@
1 1 
 Package: COTAN
2 2 
 Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 
-Version: 0.1.0
5 
-Author: Silvia Giulia Galfrè, Francesco Morandin, Marco Pietrosanto, Federico Cremisi, Manuela Helmer-Citterich
4 
+Version: 0.1.1
6 5 
 Authors@R: c(
7 6 
   person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
8 7 
   person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
9 8 
   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
10 9 
   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
11 10 
   person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
12 
-Maintainer: Galfrè Silvia Giulia <[email protected]>
13 
-Description: COTAN is a statistical and computational method to analyze the co-expression of
11 
+Description: Statistical and computational method to analyze the co-expression of
14 12 
     gene pairs at single cell level. It provides the foundation for single-cell gene
15 13 
     interactome analysis. The basic idea is studying the zero UMI counts’ distribution
16 14 
     instead of focusing on positive counts; this is done with a generalized contingency
... ... 
@@ -23,7 +21,7 @@ Description: COTAN is a statistical and computational method to analyze the co-e
23 21 
     of gene interactions and becoming a new tool to identify cell-identity marker genes.
24 22 
 URL: https://github.com/seriph78/COTAN
25 23 
 BugReports: https://github.com/seriph78/COTAN/issues
26 
-Depends: R (>= 3.5.0)
24 
+Depends: R (>= 4.0)
27 25 
 License: GPL-3
28 26 
 Encoding: UTF-8
29 27 
 RoxygenNote: 7.1.1
... ... 
@@ -34,6 +32,7 @@ Imports:
34 32 
     Matrix,
35 33 
     ggplot2,
36 34 
     ggrepel,
35 
+    stats,
37 36 
     parallel,
38 37 
     tibble,
39 38 
     tidyr,
... ... 
@@ -64,5 +63,10 @@ Config/testthat/edition: 3
64 63 
 SystemRequirements:
65 64 
     python
66 65 
 Language: en-US
66 
+biocViews:
67 
+    SystemsBiology,
68 
+    Transcriptomics,
69 
+    GeneExpression,
70 
+    SingleCell
67 71 
 VignetteBuilder: knitr
68 72 
 LazyData: true
Browse code

Solved problem for import data for examples running. Fixed latex error for \chi^2.

seriph78 authored on 27/03/2021 11:24:10
Showing 1 changed files
DESCRIPTION
History View file @ 78289d6
... ... 
@@ -9,7 +9,7 @@ Authors@R: c(
9 9 
   person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
10 10 
   person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
11 11 
   person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
12 
-Maintainer: Silvia Giulia Galfrè <[email protected]>
12 
+Maintainer: Galfrè Silvia Giulia <[email protected]>
13 13 
 Description: COTAN is a statistical and computational method to analyze the co-expression of
14 14 
     gene pairs at single cell level. It provides the foundation for single-cell gene
15 15 
     interactome analysis. The basic idea is studying the zero UMI counts’ distribution
Browse code

Data import

Description: added orcid, web site, changed license. Fixed some function imports.
Debugging the examples (seems to work!).

Created the directory for raw-data and data (used with usethat
explained in https://mvuorre.github.io/exampleRPackage/)

seriph78 authored on 30/03/2021 17:12:07
Showing 1 changed files
DESCRIPTION
History View file @ f33dabf
... ... 
@@ -3,6 +3,12 @@ Type: Package
3 3 
 Title: COexpression Tables ANalysis
4 4 
 Version: 0.1.0
5 5 
 Author: Silvia Giulia Galfrè, Francesco Morandin, Marco Pietrosanto, Federico Cremisi, Manuela Helmer-Citterich
6 
+Authors@R: c(
7 
+  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
8 
+  person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
9 
+  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
10 
+  person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
11 
+  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
6 12 
 Maintainer: Silvia Giulia Galfrè <[email protected]>
7 13 
 Description: COTAN is a statistical and computational method to analyze the co-expression of
8 14 
     gene pairs at single cell level. It provides the foundation for single-cell gene
... ... 
@@ -15,16 +21,19 @@ Description: COTAN is a statistical and computational method to analyze the co-e
15 21 
     differentiation index. Moreover, this approach provides ways to plot and cluster genes
16 22 
     according to their co-expression pattern with other genes, effectively helping the study
17 23 
     of gene interactions and becoming a new tool to identify cell-identity marker genes.
24 
+URL: https://github.com/seriph78/COTAN
25 
+BugReports: https://github.com/seriph78/COTAN/issues
18 26 
 Depends: R (>= 3.5.0)
19 
-License: CC-BY-ND 4.0
27 
+License: GPL-3
20 28 
 Encoding: UTF-8
21 29 
 RoxygenNote: 7.1.1
22 30 
 Imports:
23 31 
     dplyr,
32 
+    methods,
33 
+    grDevices,
24 34 
     Matrix,
25 35 
     ggplot2,
26 36 
     ggrepel,
27 
-    data.table,
28 37 
     parallel,
29 38 
     tibble,
30 39 
     tidyr,
... ... 
@@ -32,24 +41,25 @@ Imports:
32 41 
     reticulate,
33 42 
     ComplexHeatmap,
34 43 
     circlize,
35 
-    grid
44 
+    grid,
45 
+    scales,
46 
+    utils,
47 
+    rlang
36 48 
 Suggests:
37 49 
     testthat (>= 3.0.0),
38 50 
     spelling,
39 51 
     knitr,
52 
+    data.table,
40 53 
     rmarkdown,
41 54 
     R.utils,
42 
-    dendextend,
43 
-    Rtsne,
44 
-    plotly,
45 55 
     tidyverse,
46 56 
     htmlwidgets,
47 57 
     MASS,
48 58 
     factoextra,
49 59 
     Rtsne,
50 60 
     plotly,
51 
-    htmlwidgets,
52 
-    dendextend
61 
+    dendextend,
62 
+    cowplot
53 63 
 Config/testthat/edition: 3
54 64 
 SystemRequirements:
55 65 
     python
Browse code

Added automatic.COTAN function. Added parameter to change core number. Added example to get.expected.ct, get.observed.ct. Added a warning for the non-integer input matrix. Added lines to recreate the whole COEX matrix (stored only half). LDI changed: now it takes the 10% of genes (before was 5%)

seriph78 authored on 20/03/2021 15:56:41
Showing 1 changed files
DESCRIPTION
History View file @ 003f8c0
... ... 
@@ -27,26 +27,29 @@ Imports:
27 27 
     data.table,
28 28 
     parallel,
29 29 
     tibble,
30 
-    dplyr,
31 30 
     tidyr,
32 31 
     basilisk,
33 32 
     reticulate,
34 33 
     ComplexHeatmap,
35 
-    latex2exp
34 
+    circlize,
35 
+    grid
36 36 
 Suggests:
37 37 
     testthat (>= 3.0.0),
38 38 
     spelling,
39 39 
     knitr,
40 40 
     rmarkdown,
41 
-    data.table,
42 41 
     R.utils,
43 
-    Matrix,
44 42 
     dendextend,
45 43 
     Rtsne,
46 44 
     plotly,
47 45 
     tidyverse,
48 46 
     htmlwidgets,
49 
-    MASS
47 
+    MASS,
48 
+    factoextra,
49 
+    Rtsne,
50 
+    plotly,
51 
+    htmlwidgets,
52 
+    dendextend
50 53 
 Config/testthat/edition: 3
51 54 
 SystemRequirements:
52 55 
     python
Browse code

Added get.expected.ct and get.observed.ct. Fixed but in DESCRIPTION and added LazyData: true

seriph78 authored on 16/03/2021 17:46:42
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DESCRIPTION
History View file @ df0fe17
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@@ -31,7 +31,7 @@ Imports:
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     tidyr,
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     basilisk,
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     reticulate,
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-    ComplexHeatmap
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+    ComplexHeatmap,
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     latex2exp
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 Suggests:
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     testthat (>= 3.0.0),
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@@ -52,3 +52,4 @@ SystemRequirements:
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     python
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 Language: en-US
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 VignetteBuilder: knitr
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+LazyData: true
Browse code

Fixed a minor bug in the automatic.COTAN.object.creation function. Completed the imports for the same function.

seriph78 authored on 14/03/2021 20:19:26
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DESCRIPTION
History View file @ df3ddd0
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@@ -32,6 +32,7 @@ Imports:
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     basilisk,
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     reticulate,
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     ComplexHeatmap
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+    latex2exp
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 Suggests:
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     testthat (>= 3.0.0),
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     spelling,
Browse code

Added get.gene.coexpression.space, plot.heatmap, plot.general.heatmap, function G (to be used insted of S) corrected to manage 0ln(0). Test for get.GDI added. Added also gene_clustering vignette.

seriph78 authored on 10/03/2021 15:28:49
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DESCRIPTION
History View file @ 946a4f1
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@@ -30,7 +30,8 @@ Imports:
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     dplyr,
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     tidyr,
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     basilisk,
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-    reticulate
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+    reticulate,
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+    ComplexHeatmap
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 Suggests:
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     testthat (>= 3.0.0),
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     spelling,
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@@ -38,7 +39,13 @@ Suggests:
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     rmarkdown,
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     data.table,
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     R.utils,
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-    Matrix
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+    Matrix,
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+    dendextend,
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+    Rtsne,
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+    plotly,
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+    tidyverse,
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+    htmlwidgets,
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+    MASS
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 Config/testthat/edition: 3
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 SystemRequirements:
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     python
Browse code

Solved some issues in the importing python script. Solved some problem for the multicore function in a minimization. Started the vignette: not finished.

seriph78 authored on 06/03/2021 17:18:33
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DESCRIPTION
History View file @ 7233f48
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@@ -33,8 +33,14 @@ Imports:
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     reticulate
34 34 
 Suggests:
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     testthat (>= 3.0.0),
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-    spelling
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+    spelling,
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+    knitr,
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+    rmarkdown,
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+    data.table,
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+    R.utils,
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+    Matrix
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 Config/testthat/edition: 3
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 SystemRequirements:
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     python
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 Language: en-US
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+VignetteBuilder: knitr
Browse code

Changed the name for the R main file. Added the p-value function. Changed the COEX from old (not divided by sqrt(cell_number) to the new (as in the tesis and in the paper). Consiquently, changed also the get.S function.

seriph78 authored on 05/03/2021 11:51:29
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DESCRIPTION
History View file @ 94516a2
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@@ -4,7 +4,18 @@ Title: COexpression Tables ANalysis
4 4 
 Version: 0.1.0
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 Author: Silvia Giulia Galfrè, Francesco Morandin, Marco Pietrosanto, Federico Cremisi, Manuela Helmer-Citterich
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 Maintainer: Silvia Giulia Galfrè <[email protected]>
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-Description: COTAN is a statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts’ distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.
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+Description: COTAN is a statistical and computational method to analyze the co-expression of
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+    gene pairs at single cell level. It provides the foundation for single-cell gene
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+    interactome analysis. The basic idea is studying the zero UMI counts’ distribution
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+    instead of focusing on positive counts; this is done with a generalized contingency
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+    tables framework. COTAN can effectively assess the correlated or anti-correlated
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+    expression of gene pairs. It provides a numerical index related to the correlation and an
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+    approximate p-value for the associated independence test. COTAN can also evaluate whether
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+    single genes are differentially expressed, scoring them with a newly defined global
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+    differentiation index. Moreover, this approach provides ways to plot and cluster genes
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+    according to their co-expression pattern with other genes, effectively helping the study
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+    of gene interactions and becoming a new tool to identify cell-identity marker genes.
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+Depends: R (>= 3.5.0)
8 19 
 License: CC-BY-ND 4.0
9 20 
 Encoding: UTF-8
10 21 
 RoxygenNote: 7.1.1
Browse code

Divided the function in internal and main. Import of package/function specifically for each funtion.

seriph78 authored on 02/03/2021 07:30:20
Showing 1 changed files
DESCRIPTION
History View file @ 3e9e49c
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@@ -7,7 +7,6 @@ Maintainer: Silvia Giulia Galfrè <[email protected]>
7 7 
 Description: COTAN is a statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts’ distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.
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 License: CC-BY-ND 4.0
9 9 
 Encoding: UTF-8
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-LazyData: true
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 RoxygenNote: 7.1.1
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 Imports:
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     dplyr,
Browse code

First commit. The problem between test(), which is ok, and the test part inside chech() that does not find the files, need to be fixed. Some documentation need to be completed. Basilisk and reticulate are working.

seriph78 authored on 20/02/2021 16:05:52
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DESCRIPTION
History View file @ cd6ed08
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new file mode 100644
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@@ -0,0 +1,30 @@
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+Package: COTAN
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+Type: Package
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+Title: COexpression Tables ANalysis
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+Version: 0.1.0
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+Author: Silvia Giulia Galfrè, Francesco Morandin, Marco Pietrosanto, Federico Cremisi, Manuela Helmer-Citterich
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+Maintainer: Silvia Giulia Galfrè <[email protected]>
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+Description: COTAN is a statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts’ distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.
8 
+License: CC-BY-ND 4.0
9 
+Encoding: UTF-8
10 
+LazyData: true
11 
+RoxygenNote: 7.1.1
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+Imports:
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+    dplyr,
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+    Matrix,
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+    ggplot2,
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+    ggrepel,
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+    data.table,
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+    parallel,
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+    tibble,
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+    dplyr,
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+    tidyr,
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+    basilisk,
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+    reticulate
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+Suggests:
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+    testthat (>= 3.0.0),
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+    spelling
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+Config/testthat/edition: 3
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+SystemRequirements:
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+    python
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+Language: en-US