1. TENxIO
  2. DESCRIPTION
Browse code

TENxIO 1.11.5: Imports Seqinfo instead of GenomeInfoDb

Hervé Pagès authored on 21/06/2025 05:21:24
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DESCRIPTION
History View file @ f7f2c88
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.11.4
4 
+Version: 1.11.5
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -15,7 +15,7 @@ Imports:
15 15 
   BiocBaseUtils,
16 16 
   BiocGenerics,
17 17 
   BiocIO,
18 
-  GenomeInfoDb,
18 
+  Seqinfo,
19 19 
   GenomicRanges,
20 20 
   HDF5Array,
21 21 
   Matrix,
... ... 
@@ -32,7 +32,7 @@ Suggests:
32 32 
   DropletTestFiles,
33 33 
   ExperimentHub,
34 34 
   knitr,
35 
-  RaggedExperiment,
35 
+  RaggedExperiment (>= 1.33.3),
36 36 
   rmarkdown,
37 37 
   Rsamtools,
38 38 
   tinytest
Browse code

version bump 1.11.4

LiNk-NY authored on 08/05/2025 18:22:10
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DESCRIPTION
History View file @ 2f684b1
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.11.3
4 
+Version: 1.11.4
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.11.3

LiNk-NY authored on 06/05/2025 21:29:03
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DESCRIPTION
History View file @ 2761701
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.11.2
4 
+Version: 1.11.3
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.11.2

LiNk-NY authored on 06/05/2025 21:25:17
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DESCRIPTION
History View file @ d2ecffb
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.11.1
4 
+Version: 1.11.2
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -58,4 +58,4 @@ Collate:
58 58 
     'TENxPeaks-class.R'
59 59 
     'TENxTSV-class.R'
60 60 
     'utils.R'
61 
-Date: 2025-04-28
61 
+Date: 2025-05-06
Browse code

version bump 1.11.1

LiNk-NY authored on 28/04/2025 18:32:02
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DESCRIPTION
History View file @ 2c022dc
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.11.0
4 
+Version: 1.11.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -58,4 +58,4 @@ Collate:
58 58 
     'TENxPeaks-class.R'
59 59 
     'TENxTSV-class.R'
60 60 
     'utils.R'
61 
-Date: 2025-04-04
61 
+Date: 2025-04-28
Browse code

remove version restriction for RaggedExperiment

LiNk-NY authored on 28/04/2025 18:31:54
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DESCRIPTION
History View file @ cd803fd
... ... 
@@ -32,7 +32,7 @@ Suggests:
32 32 
   DropletTestFiles,
33 33 
   ExperimentHub,
34 34 
   knitr,
35 
-  RaggedExperiment (>= 1.29.5),
35 
+  RaggedExperiment,
36 36 
   rmarkdown,
37 37 
   Rsamtools,
38 38 
   tinytest
Browse code

minor formatting

LiNk-NY authored on 28/04/2025 18:31:38
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DESCRIPTION
History View file @ 65a03d1
... ... 
@@ -7,7 +7,10 @@ Authors@R:
7 7 
     "Marcel", "Ramos", , "[email protected]",
8 8 
     c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 9 
   )
10 
-Depends: R (>= 4.5.0), SingleCellExperiment, SummarizedExperiment
10 
+Depends:
11 
+  R (>= 4.5.0),
12 
+  SingleCellExperiment,
13 
+  SummarizedExperiment
11 14 
 Imports:
12 15 
   BiocBaseUtils,
13 16 
   BiocGenerics,
Browse code

update R version dep

LiNk-NY authored on 28/04/2025 18:31:23
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DESCRIPTION
History View file @ 9870d42
... ... 
@@ -7,7 +7,7 @@ Authors@R:
7 7 
     "Marcel", "Ramos", , "[email protected]",
8 8 
     c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 9 
   )
10 
-Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
10 
+Depends: R (>= 4.5.0), SingleCellExperiment, SummarizedExperiment
11 11 
 Imports:
12 12 
   BiocBaseUtils,
13 13 
   BiocGenerics,
Browse code

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

A Wokaty authored on 15/04/2025 16:57:57
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DESCRIPTION
History View file @ 742c58f
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.10.0
4 
+Version: 1.11.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
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 16:57:57
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DESCRIPTION
History View file @ 15149a7
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.9.5
4 
+Version: 1.10.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.9.5

LiNk-NY authored on 04/04/2025 19:43:30
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DESCRIPTION
History View file @ 1c6bd1a
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.9.4
4 
+Version: 1.9.5
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -55,4 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
-Date: 2024-12-05
58 
+Date: 2025-04-04
Browse code

version bump 1.9.4

LiNk-NY authored on 05/12/2024 20:58:43
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DESCRIPTION
History View file @ eb0e076
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.9.3
4 
+Version: 1.9.4
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -55,4 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
-Date: 2024-11-13
58 
+Date: 2024-12-05
Browse code

version bump 1.9.3

LiNk-NY authored on 21/11/2024 16:36:51
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DESCRIPTION
History View file @ c6c5a73
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.9.2
4 
+Version: 1.9.3
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.9.2

LiNk-NY authored on 13/11/2024 17:08:05
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DESCRIPTION
History View file @ 7ba4097
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.9.1
4 
+Version: 1.9.2
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.9.1

LiNk-NY authored on 13/11/2024 16:47:21
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DESCRIPTION
History View file @ 084c519
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.9.0
4 
+Version: 1.9.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -55,4 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
-Date: 2024-10-18
58 
+Date: 2024-11-13
Browse code

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

J Wokaty authored on 29/10/2024 15:15:20
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DESCRIPTION
History View file @ 17144f7
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.8.0
4 
+Version: 1.9.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
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 15:15:20
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DESCRIPTION
History View file @ 00bf455
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.10
4 
+Version: 1.8.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.7.10

LiNk-NY authored on 18/10/2024 22:04:29
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DESCRIPTION
History View file @ f88355b
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.9
4 
+Version: 1.7.10
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -55,4 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
-Date: 2024-10-02
58 
+Date: 2024-10-18
Browse code

add metadata methods and append to outputs

LiNk-NY authored on 18/10/2024 22:04:04
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DESCRIPTION
History View file @ a3f528a
... ... 
@@ -29,7 +29,7 @@ Suggests:
29 29 
   DropletTestFiles,
30 30 
   ExperimentHub,
31 31 
   knitr,
32 
-  RaggedExperiment,
32 
+  RaggedExperiment (>= 1.29.5),
33 33 
   rmarkdown,
34 34 
   Rsamtools,
35 35 
   tinytest
Browse code

version bump 1.7.9

LiNk-NY authored on 17/10/2024 18:26:36
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DESCRIPTION
History View file @ a8220df
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.8
4 
+Version: 1.7.9
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.7.8

LiNk-NY authored on 02/10/2024 19:33:55
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DESCRIPTION
History View file @ 617cf3c
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.7
4 
+Version: 1.7.8
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -55,4 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
-Date: 2024-09-19
58 
+Date: 2024-10-02
Browse code

version bump 1.7.7

LiNk-NY authored on 23/09/2024 20:47:44
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DESCRIPTION
History View file @ 7b86cc1
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.6
4 
+Version: 1.7.7
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.7.6

LiNk-NY authored on 19/09/2024 18:11:56
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DESCRIPTION
History View file @ 5bb03e0
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.5
4 
+Version: 1.7.6
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
... ... 
@@ -55,4 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
-Date: 2024-08-22
58 
+Date: 2024-09-19
Browse code

move rhdf5 and HDF5Array from Suggests to Imports

LiNk-NY authored on 19/09/2024 18:11:49
Showing 1 changed files
DESCRIPTION
History View file @ 734ba0a
... ... 
@@ -14,11 +14,13 @@ Imports:
14 14 
   BiocIO,
15 15 
   GenomeInfoDb,
16 16 
   GenomicRanges,
17 
+  HDF5Array,
17 18 
   Matrix,
18 19 
   MatrixGenerics,
19 20 
   methods,
20 21 
   RCurl,
21 22 
   readr,
23 
+  rhdf5,
22 24 
   R.utils,
23 25 
   S4Vectors,
24 26 
   utils
... ... 
@@ -26,10 +28,8 @@ Suggests:
26 28 
   BiocStyle,
27 29 
   DropletTestFiles,
28 30 
   ExperimentHub,
29 
-  HDF5Array,
30 31 
   knitr,
31 32 
   RaggedExperiment,
32 
-  rhdf5,
33 33 
   rmarkdown,
34 34 
   Rsamtools,
35 35 
   tinytest
Browse code

version bump 1.7.5

LiNk-NY authored on 19/09/2024 14:33:14
Showing 1 changed files
DESCRIPTION
History View file @ 48dc1d3
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.4
4 
+Version: 1.7.5
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.7.4

LiNk-NY authored on 11/09/2024 12:34:09
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DESCRIPTION
History View file @ 172f383
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.3
4 
+Version: 1.7.4
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.7.3

LiNk-NY authored on 30/08/2024 19:27:33
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DESCRIPTION
History View file @ 40844df
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.2
4 
+Version: 1.7.3
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

import rowData for version 3 datasets

LiNk-NY authored on 29/08/2024 22:05:11 • LiNk-NY committed on 30/08/2024 18:29:22
Showing 1 changed files
DESCRIPTION
History View file @ 99f9955
... ... 
@@ -42,7 +42,7 @@ VignetteBuilder: knitr
42 42 
 License: Artistic-2.0
43 43 
 Encoding: UTF-8
44 44 
 Roxygen: list(markdown = TRUE)
45 
-RoxygenNote: 7.2.3
45 
+RoxygenNote: 7.3.2
46 46 
 BugReports: https://github.com/waldronlab/TENxIO/issues
47 47 
 URL: https://github.com/waldronlab/TENxIO
48 48 
 Collate:
Browse code

version bump 1.7.2

LiNk-NY authored on 22/08/2024 19:36:28
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DESCRIPTION
History View file @ f43ab60
... ... 
@@ -1,10 +1,10 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.1
4 
+Version: 1.7.2
5 5 
 Authors@R:
6 6 
   person(
7 
-    "Marcel", "Ramos", , "[email protected]",
7 
+    "Marcel", "Ramos", , "[email protected]",
8 8 
     c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 9 
   )
10 10 
 Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
... ... 
@@ -55,3 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'utils.R'
58 
+Date: 2024-08-22
Browse code

version bump 1.7.1

LiNk-NY authored on 05/06/2024 20:11:33
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DESCRIPTION
History View file @ 47ccab2
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.7.0
4 
+Version: 1.7.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 15:45:22
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DESCRIPTION
History View file @ 79a7378
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.6.0
4 
+Version: 1.7.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 15:45:22
Showing 1 changed files
DESCRIPTION
History View file @ 2372980
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.4
4 
+Version: 1.6.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.5.4

LiNk-NY authored on 24/04/2024 21:51:10
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DESCRIPTION
History View file @ 30b79e5
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.3
4 
+Version: 1.5.4
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.5.3

LiNk-NY authored on 20/11/2023 19:40:35
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DESCRIPTION
History View file @ 2718164
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.0
4 
+Version: 1.5.3
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

Revert "add TENxSpatialList"

This reverts commit 2cade115d2b834477e5b3e198b7b5e813244f105.

LiNk-NY authored on 20/11/2023 16:36:52
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DESCRIPTION
History View file @ 4bd2c4c
... ... 
@@ -54,5 +54,4 @@ Collate:
54 54 
     'TENxMTX-class.R'
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 
-    'TENxSpatialList-class.R'
58 57 
     'utils.R'
Browse code

Revert "update TENxVisium class"

This reverts commit 39163c4538573ae092e7497f2951fbba1929ce1b.

LiNk-NY authored on 20/11/2023 16:36:51
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DESCRIPTION
History View file @ 39cb05e
... ... 
@@ -55,6 +55,4 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'TENxSpatialList-class.R'
58 
-    'TENxSpatialCSV.R'
59 
-    'TENxVisium-class.R'
60 58 
     'utils.R'
Browse code

Revert "document classes and constructors"

This reverts commit face862e90e3c3df4f5dd39d05efac23dc237c08.

LiNk-NY authored on 20/11/2023 16:36:46
Showing 1 changed files
DESCRIPTION
History View file @ be3e0ee
... ... 
@@ -14,7 +14,6 @@ Imports:
14 14 
   BiocIO,
15 15 
   GenomeInfoDb,
16 16 
   GenomicRanges,
17 
-  jsonlite,
18 17 
   Matrix,
19 18 
   MatrixGenerics,
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   methods,
... ... 
@@ -22,7 +21,6 @@ Imports:
22 21 
   readr,
23 22 
   R.utils,
24 23 
   S4Vectors,
25 
-  SpatialExperiment,
26 24 
   utils
27 25 
 Suggests:
28 26 
   BiocStyle,
... ... 
@@ -55,8 +53,8 @@ Collate:
55 53 
     'TENxIO-package.R'
56 54 
     'TENxMTX-class.R'
57 55 
     'TENxPeaks-class.R'
58 
-    'TENxSpatialCSV.R'
59 
-    'TENxSpatialList-class.R'
60 56 
     'TENxTSV-class.R'
57 
+    'TENxSpatialList-class.R'
58 
+    'TENxSpatialCSV.R'
61 59 
     'TENxVisium-class.R'
62 60 
     'utils.R'
Browse code

Revert "version bump 1.5.1"

This reverts commit de2966fa521164f2129c0ac922f897d40c7a9747.

LiNk-NY authored on 20/11/2023 16:28:53
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.1
4 
+Version: 1.5.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

Revert "version bump 1.5.2"

This reverts commit 2c30cef36d4274494dd58ce90844321fc216af89.

LiNk-NY authored on 20/11/2023 16:28:46
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DESCRIPTION
History View file @ 2314a48
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.2
4 
+Version: 1.5.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.5.2

LiNk-NY authored on 26/10/2023 18:50:30
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DESCRIPTION
History View file @ 2c30cef
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.1
4 
+Version: 1.5.2
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.5.1

LiNk-NY authored on 25/10/2023 00:11:11
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DESCRIPTION
History View file @ de2966f
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.5.0
4 
+Version: 1.5.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

document classes and constructors

LiNk-NY authored on 12/10/2023 20:56:54
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DESCRIPTION
History View file @ face862
... ... 
@@ -14,6 +14,7 @@ Imports:
14 14 
   BiocIO,
15 15 
   GenomeInfoDb,
16 16 
   GenomicRanges,
17 
+  jsonlite,
17 18 
   Matrix,
18 19 
   MatrixGenerics,
19 20 
   methods,
... ... 
@@ -21,6 +22,7 @@ Imports:
21 22 
   readr,
22 23 
   R.utils,
23 24 
   S4Vectors,
25 
+  SpatialExperiment,
24 26 
   utils
25 27 
 Suggests:
26 28 
   BiocStyle,
... ... 
@@ -53,8 +55,8 @@ Collate:
53 55 
     'TENxIO-package.R'
54 56 
     'TENxMTX-class.R'
55 57 
     'TENxPeaks-class.R'
56 
-    'TENxTSV-class.R'
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-    'TENxSpatialList-class.R'
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     'TENxSpatialCSV.R'
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+    'TENxSpatialList-class.R'
60 
+    'TENxTSV-class.R'
59 61 
     'TENxVisium-class.R'
60 62 
     'utils.R'
Browse code

update TENxVisium class

LiNk-NY authored on 28/09/2023 19:58:47 • LiNk-NY committed on 25/10/2023 00:04:07
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DESCRIPTION
History View file @ 39163c4
... ... 
@@ -55,4 +55,6 @@ Collate:
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 57 
     'TENxSpatialList-class.R'
58 
+    'TENxSpatialCSV.R'
59 
+    'TENxVisium-class.R'
58 60 
     'utils.R'
Browse code

add TENxSpatialList

LiNk-NY authored on 27/09/2023 21:02:19 • LiNk-NY committed on 25/10/2023 00:04:07
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DESCRIPTION
History View file @ 2cade11
... ... 
@@ -54,4 +54,5 @@ Collate:
54 54 
     'TENxMTX-class.R'
55 55 
     'TENxPeaks-class.R'
56 56 
     'TENxTSV-class.R'
57 
+    'TENxSpatialList-class.R'
57 58 
     'utils.R'
Browse code

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

J Wokaty authored on 24/10/2023 15:44:46
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DESCRIPTION
History View file @ e949113
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.4.0
4 
+Version: 1.5.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
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 15:44:46
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DESCRIPTION
History View file @ bd46e64
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.3.1
4 
+Version: 1.4.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.3.1

LiNk-NY authored on 12/09/2023 14:37:12
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DESCRIPTION
History View file @ 99539de
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.3.0
4 
+Version: 1.3.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

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

J Wokaty authored on 25/04/2023 15:40:51
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DESCRIPTION
History View file @ 43b0211
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.2.0
4 
+Version: 1.3.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
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 15:40:51
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DESCRIPTION
History View file @ f2ae1a5
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.1.3
4 
+Version: 1.2.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.1.3

LiNk-NY authored on 27/02/2023 20:32:27
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DESCRIPTION
History View file @ 121daf5
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.1.2
4 
+Version: 1.1.3
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.1.2

LiNk-NY authored on 10/02/2023 17:09:44
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DESCRIPTION
History View file @ 41434f2
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 1.1.1
4 
+Version: 1.1.2
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 1.1.1

LiNk-NY authored on 19/01/2023 21:56:28
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DESCRIPTION
History View file @ 428a405
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
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-Version: 1.1.0
4 
+Version: 1.1.1
5 5 
 Authors@R:
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   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

include TENxTSV and export

LiNk-NY authored on 19/01/2023 21:23:59
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DESCRIPTION
History View file @ f8bfe71
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@@ -53,4 +53,5 @@ Collate:
53 53 
     'TENxIO-package.R'
54 54 
     'TENxMTX-class.R'
55 55 
     'TENxPeaks-class.R'
56 
+    'TENxTSV-class.R'
56 57 
     'utils.R'
Browse code

update roxygen version

LiNk-NY authored on 19/01/2023 21:11:45
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DESCRIPTION
History View file @ a542288
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@@ -42,7 +42,7 @@ VignetteBuilder: knitr
42 42 
 License: Artistic-2.0
43 43 
 Encoding: UTF-8
44 44 
 Roxygen: list(markdown = TRUE)
45 
-RoxygenNote: 7.2.1
45 
+RoxygenNote: 7.2.3
46 46 
 BugReports: https://github.com/waldronlab/TENxIO/issues
47 47 
 URL: https://github.com/waldronlab/TENxIO
48 48 
 Collate:
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:27:43
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DESCRIPTION
History View file @ 4b38b34
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
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-Version: 1.0.0
4 
+Version: 1.1.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:27:43
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DESCRIPTION
History View file @ 057c32b
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.10
4 
+Version: 1.0.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.99.10

LiNk-NY authored on 27/10/2022 14:19:18
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DESCRIPTION
History View file @ 7a0f3e5
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.9
4 
+Version: 0.99.10
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.99.9

LiNk-NY authored on 21/10/2022 14:33:52
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DESCRIPTION
History View file @ e51787a
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.8
4 
+Version: 0.99.9
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.99.8

LiNk-NY authored on 21/10/2022 14:27:44
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DESCRIPTION
History View file @ 82f7841
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.7
4 
+Version: 0.99.8
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.99.7

LiNk-NY authored on 18/10/2022 18:27:38
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DESCRIPTION
History View file @ a4d61b6
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
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-Version: 0.99.6
4 
+Version: 0.99.7
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.99.6

LiNk-NY authored on 18/10/2022 17:33:03
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DESCRIPTION
History View file @ 12ed99b
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
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-Version: 0.99.5
4 
+Version: 0.99.6
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

add longtests directory

LiNk-NY authored on 17/10/2022 22:43:48
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DESCRIPTION
History View file @ be9e42a
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@@ -24,6 +24,7 @@ Imports:
24 24 
   utils
25 25 
 Suggests:
26 26 
   BiocStyle,
27 
+  DropletTestFiles,
27 28 
   ExperimentHub,
28 29 
   HDF5Array,
29 30 
   knitr,
Browse code

version bump 0.99.5

LiNk-NY authored on 06/10/2022 15:16:58
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DESCRIPTION
History View file @ 0559301
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.4
4 
+Version: 0.99.5
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

update docs and spellcheck

LiNk-NY authored on 05/10/2022 22:01:03
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DESCRIPTION
History View file @ 093a650
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@@ -34,7 +34,7 @@ Suggests:
34 34 
   tinytest
35 35 
 Description: Provides a structured S4 approach to importing data files from
36 36 
   the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene
37 
-  Expresssion data among other data types. The main Bioconductor data
37 
+  Expression data among other data types. The main Bioconductor data
38 38 
   representations used are SingleCellExperiment and RaggedExperiment.
39 39 
 biocViews: Software, Infrastructure, DataImport, SingleCell
40 40 
 VignetteBuilder: knitr
Browse code

version bump 0.99.4

LiNk-NY authored on 16/09/2022 16:08:26
Showing 1 changed files
DESCRIPTION
History View file @ 6124684
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.3
4 
+Version: 0.99.4
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.99.3

LiNk-NY authored on 24/08/2022 22:58:44
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DESCRIPTION
History View file @ 86862c0
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.2
4 
+Version: 0.99.3
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

use VignetteBuilder field in DESCRIPTION

LiNk-NY authored on 24/08/2022 22:58:00
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DESCRIPTION
History View file @ 3db808b
... ... 
@@ -37,6 +37,7 @@ Description: Provides a structured S4 approach to importing data files from
37 37 
   Expresssion data among other data types. The main Bioconductor data
38 38 
   representations used are SingleCellExperiment and RaggedExperiment.
39 39 
 biocViews: Software, Infrastructure, DataImport, SingleCell
40 
+VignetteBuilder: knitr
40 41 
 License: Artistic-2.0
41 42 
 Encoding: UTF-8
42 43 
 Roxygen: list(markdown = TRUE)
Browse code

add appropriate imports

LiNk-NY authored on 24/08/2022 22:57:28
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DESCRIPTION
History View file @ 30e1224
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@@ -36,7 +36,7 @@ Description: Provides a structured S4 approach to importing data files from
36 36 
   the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene
37 37 
   Expresssion data among other data types. The main Bioconductor data
38 38 
   representations used are SingleCellExperiment and RaggedExperiment.
39 
-biocViews: Software, Infrastructure, DataImport
39 
+biocViews: Software, Infrastructure, DataImport, SingleCell
40 40 
 License: Artistic-2.0
41 41 
 Encoding: UTF-8
42 42 
 Roxygen: list(markdown = TRUE)
Browse code

bump version 0.99.2

LiNk-NY authored on 24/08/2022 22:14:02
Showing 1 changed files
DESCRIPTION
History View file @ 52ad135
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.1
4 
+Version: 0.99.2
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

bump version 0.99.1

LiNk-NY authored on 24/08/2022 22:07:06
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DESCRIPTION
History View file @ ea81ad7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.99.0
4 
+Version: 0.99.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

add biocViews

LiNk-NY authored on 24/08/2022 21:22:27
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DESCRIPTION
History View file @ b9af2ed
... ... 
@@ -36,6 +36,7 @@ Description: Provides a structured S4 approach to importing data files from
36 36 
   the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene
37 37 
   Expresssion data among other data types. The main Bioconductor data
38 38 
   representations used are SingleCellExperiment and RaggedExperiment.
39 
+biocViews: Software, Infrastructure, DataImport
39 40 
 License: Artistic-2.0
40 41 
 Encoding: UTF-8
41 42 
 Roxygen: list(markdown = TRUE)
Browse code

pre-submission version bump

LiNk-NY authored on 24/08/2022 21:10:20
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DESCRIPTION
History View file @ fa0e2b6
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.13.0
4 
+Version: 0.99.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

add tinytest to Suggests and import setSlots

LiNk-NY authored on 24/08/2022 21:09:58
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DESCRIPTION
History View file @ aa3ee6c
... ... 
@@ -30,7 +30,8 @@ Suggests:
30 30 
   RaggedExperiment,
31 31 
   rhdf5,
32 32 
   rmarkdown,
33 
-  Rsamtools
33 
+  Rsamtools,
34 
+  tinytest
34 35 
 Description: Provides a structured S4 approach to importing data files from
35 36 
   the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene
36 37 
   Expresssion data among other data types. The main Bioconductor data
Browse code

version bump 1.13.0

LiNk-NY authored on 16/08/2022 16:47:34
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DESCRIPTION
History View file @ fe67127
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
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 Title: Import methods for 10X Genomics files
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-Version: 0.12.0
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+Version: 0.13.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.12.0

LiNk-NY authored on 15/08/2022 20:54:06
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DESCRIPTION
History View file @ f8c37a9
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
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3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.11.0
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+Version: 0.12.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

enable remote HDF5 files

LiNk-NY authored on 15/08/2022 20:14:17
Showing 1 changed files
DESCRIPTION
History View file @ 76e591e
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@@ -19,6 +19,7 @@ Imports:
19 19 
   methods,
20 20 
   RCurl,
21 21 
   readr,
22 
+  R.utils,
22 23 
   S4Vectors,
23 24 
   utils
24 25 
 Suggests:
Browse code

Merge branch 'devel' of github.com:waldronlab/TENxIO into devel

LiNk-NY authored on 03/08/2022 19:50:21
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Browse code

version bump 0.11.0

LiNk-NY authored on 03/08/2022 19:49:24
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DESCRIPTION
History View file @ 1189e6a
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.10.0
4 
+Version: 0.11.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

add ExperimentHub to Suggests

LiNk-NY authored on 03/08/2022 19:49:02
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DESCRIPTION
History View file @ ae898bd
... ... 
@@ -23,6 +23,7 @@ Imports:
23 23 
   utils
24 24 
 Suggests:
25 25 
   BiocStyle,
26 
+  ExperimentHub,
26 27 
   HDF5Array,
27 28 
   knitr,
28 29 
   RaggedExperiment,
Browse code

roxygen bump

LiNk-NY authored on 03/08/2022 14:30:01
Showing 1 changed files
DESCRIPTION
History View file @ cb22f9e
... ... 
@@ -36,7 +36,7 @@ Description: The package exports methods for working with version 2 and 3 of
36 36 
 License: Artistic-2.0
37 37 
 Encoding: UTF-8
38 38 
 Roxygen: list(markdown = TRUE)
39 
-RoxygenNote: 7.2.0
39 
+RoxygenNote: 7.2.1
40 40 
 BugReports: https://github.com/waldronlab/TENxIO/issues
41 41 
 URL: https://github.com/waldronlab/TENxIO
42 42 
 Collate:
Browse code

version bump 0.10.1

LiNk-NY authored on 27/07/2022 17:38:07
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DESCRIPTION
History View file @ 1634d7a
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.10.0
4 
+Version: 0.10.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

update Description field

LiNk-NY authored on 27/07/2022 17:38:04
Showing 1 changed files
DESCRIPTION
History View file @ 2b50d2c
... ... 
@@ -29,10 +29,10 @@ Suggests:
29 29 
   rhdf5,
30 30 
   rmarkdown,
31 31 
   Rsamtools
32 
-Description: The package exports methods for working with version 2 and 3 of
33 
-    10X Genomics files. It simplifies importing by creating a class with
34 
-    slots for version and group in the H5 file. Currently only H5 files are
35 
-    supported.
32 
+Description: Provides a structured S4 approach to importing data files from
33 
+  the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene
34 
+  Expresssion data among other data types. The main Bioconductor data
35 
+  representations used are SingleCellExperiment and RaggedExperiment.
36 36 
 License: Artistic-2.0
37 37 
 Encoding: UTF-8
38 38 
 Roxygen: list(markdown = TRUE)
Browse code

version bump 0.10.0

LiNk-NY authored on 21/07/2022 21:47:40
Showing 1 changed files
DESCRIPTION
History View file @ db61166
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.9.0
4 
+Version: 0.10.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.9.0

LiNk-NY authored on 15/07/2022 21:42:35
Showing 1 changed files
DESCRIPTION
History View file @ 27bb9b8
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.8.0
4 
+Version: 0.9.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.8.0

LiNk-NY authored on 14/07/2022 16:58:54
Showing 1 changed files
DESCRIPTION
History View file @ df2b429
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.7.0
4 
+Version: 0.8.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.7.0

LiNk-NY authored on 14/07/2022 02:33:36
Showing 1 changed files
DESCRIPTION
History View file @ 8f37889
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.6.0
4 
+Version: 0.7.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

Remove SingleCellMultiModal from dependencies, not used

LiNk-NY authored on 14/07/2022 02:31:10
Showing 1 changed files
DESCRIPTION
History View file @ e658b86
... ... 
@@ -20,7 +20,6 @@ Imports:
20 20 
   RCurl,
21 21 
   readr,
22 22 
   S4Vectors,
23 
-  SingleCellMultiModal,
24 23 
   utils
25 24 
 Suggests:
26 25 
   BiocStyle,
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add TENxIO-package.R and doc

LiNk-NY authored on 28/06/2022 19:58:14
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DESCRIPTION
History View file @ 9a7aba1
... ... 
@@ -45,6 +45,7 @@ Collate:
45 45 
     'TENxFileList-class.R'
46 46 
     'TENxFragments-class.R'
47 47 
     'TENxH5-class.R'
48 
+    'TENxIO-package.R'
48 49 
     'TENxMTX-class.R'
49 50 
     'TENxPeaks-class.R'
50 51 
     'utils.R'
Browse code

version bump

LiNk-NY authored on 28/06/2022 16:48:09
Showing 1 changed files
DESCRIPTION
History View file @ 098cd4c
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.5.0
4 
+Version: 0.6.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

export MTX class and update docs

LiNk-NY authored on 28/06/2022 16:47:36
Showing 1 changed files
DESCRIPTION
History View file @ 990c3a2
... ... 
@@ -38,6 +38,8 @@ License: Artistic-2.0
38 38 
 Encoding: UTF-8
39 39 
 Roxygen: list(markdown = TRUE)
40 40 
 RoxygenNote: 7.2.0
41 
+BugReports: https://github.com/waldronlab/TENxIO/issues
42 
+URL: https://github.com/waldronlab/TENxIO
41 43 
 Collate:
42 44 
     'TENxFile-class.R'
43 45 
     'TENxFileList-class.R'
Browse code

version bump 0.5.0

LiNk-NY authored on 28/06/2022 16:25:27
Showing 1 changed files
DESCRIPTION
History View file @ 9efd93b
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.4.2
4 
+Version: 0.5.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

check existence with file.exists or url.exists

LiNk-NY authored on 28/06/2022 16:23:33
Showing 1 changed files
DESCRIPTION
History View file @ 1827e3a
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@@ -17,6 +17,7 @@ Imports:
17 17 
   Matrix,
18 18 
   MatrixGenerics,
19 19 
   methods,
20 
+  RCurl,
20 21 
   readr,
21 22 
   S4Vectors,
22 23 
   SingleCellMultiModal,
Browse code

version bump 0.4.2

LiNk-NY authored on 24/06/2022 21:41:04
Showing 1 changed files
DESCRIPTION
History View file @ b6ea7e0
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.4.1
4 
+Version: 0.4.2
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump

LiNk-NY authored on 22/06/2022 19:04:07
Showing 1 changed files
DESCRIPTION
History View file @ 97b8665
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.4.0
4 
+Version: 0.4.1
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump

LiNk-NY authored on 16/06/2022 18:06:26
Showing 1 changed files
DESCRIPTION
History View file @ 6a762f7
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@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.3.0
4 
+Version: 0.4.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

version bump 0.3.0

LiNk-NY authored on 14/06/2022 16:54:32
Showing 1 changed files
DESCRIPTION
History View file @ 62d8295
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.2.0
4 
+Version: 0.3.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

remove experimental ShellExperiment

LiNk-NY authored on 14/06/2022 16:52:59
Showing 1 changed files
DESCRIPTION
History View file @ 4ed8a9a
... ... 
@@ -39,10 +39,9 @@ Roxygen: list(markdown = TRUE)
39 39 
 RoxygenNote: 7.2.0
40 40 
 Collate:
41 41 
     'TENxFile-class.R'
42 
-    'TENxH5-class.R'
43 
-    'ShellExperiment-class.R'
44 42 
     'TENxFileList-class.R'
45 43 
     'TENxFragments-class.R'
44 
+    'TENxH5-class.R'
46 45 
     'TENxMTX-class.R'
47 46 
     'TENxPeaks-class.R'
48 47 
     'utils.R'
Browse code

use .setNames when only one unique genome

LiNk-NY authored on 09/06/2022 19:25:24
Showing 1 changed files
DESCRIPTION
History View file @ f19edc9
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@@ -41,7 +41,6 @@ Collate:
41 41 
     'TENxFile-class.R'
42 42 
     'TENxH5-class.R'
43 43 
     'ShellExperiment-class.R'
44 
-    'TENxFile-methods.R'
45 44 
     'TENxFileList-class.R'
46 45 
     'TENxFragments-class.R'
47 46 
     'TENxMTX-class.R'
Browse code

include ShellExperiment class

LiNk-NY authored on 09/06/2022 18:33:12
Showing 1 changed files
DESCRIPTION
History View file @ ce7d3a7
... ... 
@@ -9,6 +9,7 @@ Authors@R:
9 9 
   )
10 10 
 Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
11 11 
 Imports:
12 
+  BiocBaseUtils,
12 13 
   BiocGenerics,
13 14 
   BiocIO,
14 15 
   GenomeInfoDb,
... ... 
@@ -36,4 +37,13 @@ License: Artistic-2.0
36 37 
 Encoding: UTF-8
37 38 
 Roxygen: list(markdown = TRUE)
38 39 
 RoxygenNote: 7.2.0
39 
-
40 
+Collate:
41 
+    'TENxFile-class.R'
42 
+    'TENxH5-class.R'
43 
+    'ShellExperiment-class.R'
44 
+    'TENxFile-methods.R'
45 
+    'TENxFileList-class.R'
46 
+    'TENxFragments-class.R'
47 
+    'TENxMTX-class.R'
48 
+    'TENxPeaks-class.R'
49 
+    'utils.R'
Browse code

follow dimnames contract

LiNk-NY authored on 09/06/2022 16:45:51
Showing 1 changed files
DESCRIPTION
History View file @ c227f9d
... ... 
@@ -13,7 +13,6 @@ Imports:
13 13 
   BiocIO,
14 14 
   GenomeInfoDb,
15 15 
   GenomicRanges,
16 
-  IRanges,
17 16 
   Matrix,
18 17 
   MatrixGenerics,
19 18 
   methods,
Browse code

use x instead of con, include row col idx

LiNk-NY authored on 09/06/2022 14:52:43
Showing 1 changed files
DESCRIPTION
History View file @ c37f993
... ... 
@@ -13,6 +13,7 @@ Imports:
13 13 
   BiocIO,
14 14 
   GenomeInfoDb,
15 15 
   GenomicRanges,
16 
+  IRanges,
16 17 
   Matrix,
17 18 
   MatrixGenerics,
18 19 
   methods,
Browse code

bump version 0.2.0

LiNk-NY authored on 03/06/2022 15:48:04
Showing 1 changed files
DESCRIPTION
History View file @ d958383
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: TENxIO
2 2 
 Type: Package
3 3 
 Title: Import methods for 10X Genomics files
4 
-Version: 0.1.0
4 
+Version: 0.2.0
5 5 
 Authors@R:
6 6 
   person(
7 7 
     "Marcel", "Ramos", , "[email protected]",
Browse code

update Imports and Suggests

LiNk-NY authored on 03/06/2022 15:04:56
Showing 1 changed files
DESCRIPTION
History View file @ d024a47
... ... 
@@ -12,6 +12,7 @@ Imports:
12 12 
   BiocGenerics,
13 13 
   BiocIO,
14 14 
   GenomeInfoDb,
15 
+  GenomicRanges,
15 16 
   Matrix,
16 17 
   MatrixGenerics,
17 18 
   methods,
... ... 
@@ -23,12 +24,16 @@ Suggests:
23 24 
   BiocStyle,
24 25 
   HDF5Array,
25 26 
   knitr,
27 
+  RaggedExperiment,
26 28 
   rhdf5,
27 
-  rmarkdown
29 
+  rmarkdown,
30 
+  Rsamtools
28 31 
 Description: The package exports methods for working with version 2 and 3 of
29 32 
     10X Genomics files. It simplifies importing by creating a class with
30 33 
     slots for version and group in the H5 file. Currently only H5 files are
31 34 
     supported.
32 35 
 License: Artistic-2.0
33 36 
 Encoding: UTF-8
37 
+Roxygen: list(markdown = TRUE)
34 38 
 RoxygenNote: 7.2.0
39 
+
Browse code

organize files

LiNk-NY authored on 02/06/2022 14:44:32
Showing 1 changed files
DESCRIPTION
History View file @ 32c59e7
... ... 
@@ -32,9 +32,3 @@ Description: The package exports methods for working with version 2 and 3 of
32 32 
 License: Artistic-2.0
33 33 
 Encoding: UTF-8
34 34 
 RoxygenNote: 7.2.0
35 
-Collate:
36 
-    'TENxFile-class.R'
37 
-    'TENxFileList-class.R'
38 
-    'TENxFile-methods.R'
39 
-    'TENxH5-class.R'
40 
-    'utils.R'
Browse code

move H5 class and methods to separate file

LiNk-NY authored on 02/06/2022 14:35:03
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DESCRIPTION
History View file @ b12b4dd
... ... 
@@ -36,4 +36,5 @@ Collate:
36 36 
     'TENxFile-class.R'
37 37 
     'TENxFileList-class.R'
38 38 
     'TENxFile-methods.R'
39 
+    'TENxH5-class.R'
39 40 
     'utils.R'
Browse code

wip: update TENxFileList class

LiNk-NY authored on 26/05/2022 21:27:12
Showing 1 changed files
DESCRIPTION
History View file @ 652d99d
... ... 
@@ -32,3 +32,8 @@ Description: The package exports methods for working with version 2 and 3 of
32 32 
 License: Artistic-2.0
33 33 
 Encoding: UTF-8
34 34 
 RoxygenNote: 7.2.0
35 
+Collate:
36 
+    'TENxFile-class.R'
37 
+    'TENxFileList-class.R'
38 
+    'TENxFile-methods.R'
39 
+    'utils.R'
Browse code

include additional packages

LiNk-NY authored on 25/05/2022 20:02:43
Showing 1 changed files
DESCRIPTION
History View file @ 926eb11
... ... 
@@ -12,8 +12,10 @@ Imports:
12 12 
   BiocGenerics,
13 13 
   BiocIO,
14 14 
   GenomeInfoDb,
15 
+  Matrix,
15 16 
   MatrixGenerics,
16 17 
   methods,
18 
+  readr,
17 19 
   S4Vectors,
18 20 
   SingleCellMultiModal,
19 21 
   utils
... ... 
@@ -29,4 +31,4 @@ Description: The package exports methods for working with version 2 and 3 of
29 31 
     supported.
30 32 
 License: Artistic-2.0
31 33 
 Encoding: UTF-8
32 
-RoxygenNote: 7.1.2
34 
+RoxygenNote: 7.2.0
Browse code

update imports

LiNk-NY authored on 24/05/2022 21:48:34
Showing 1 changed files
DESCRIPTION
History View file @ 2a8afd3
... ... 
@@ -7,12 +7,13 @@ Authors@R:
7 7 
     "Marcel", "Ramos", , "[email protected]",
8 8 
     c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 9 
   )
10 
-Depends: R (>= 4.2.0)
10 
+Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
11 11 
 Imports:
12 12 
   BiocGenerics,
13 13 
   BiocIO,
14 14 
   GenomeInfoDb,
15 15 
   MatrixGenerics,
16 
+  methods,
16 17 
   S4Vectors,
17 18 
   SingleCellMultiModal,
18 19 
   utils
Browse code

update DESC

LiNk-NY authored on 24/05/2022 21:12:34
Showing 1 changed files
DESCRIPTION
History View file @ 857b82d
... ... 
@@ -14,11 +14,12 @@ Imports:
14 14 
   GenomeInfoDb,
15 15 
   MatrixGenerics,
16 16 
   S4Vectors,
17 
-  SingleCellMultiModal
17 
+  SingleCellMultiModal,
18 
+  utils
18 19 
 Suggests:
19 20 
   BiocStyle,
20 21 
   HDF5Array,
21 
-  knit,
22 
+  knitr,
22 23 
   rhdf5,
23 24 
   rmarkdown
24 25 
 Description: The package exports methods for working with version 2 and 3 of
Browse code

Update imports

LiNk-NY authored on 24/05/2022 21:04:33
Showing 1 changed files
DESCRIPTION
History View file @ 427e077
... ... 
@@ -8,8 +8,19 @@ Authors@R:
8 8 
     c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 9 
   )
10 10 
 Depends: R (>= 4.2.0)
11 
-Imports: BiocIO, BiocGenerics, MatrixGenerics, GenomeInfoDb,
12 
-  SingleCellMultiModal, S4Vectors
11 
+Imports:
12 
+  BiocGenerics,
13 
+  BiocIO,
14 
+  GenomeInfoDb,
15 
+  MatrixGenerics,
16 
+  S4Vectors,
17 
+  SingleCellMultiModal
18 
+Suggests:
19 
+  BiocStyle,
20 
+  HDF5Array,
21 
+  knit,
22 
+  rhdf5,
23 
+  rmarkdown
13 24 
 Description: The package exports methods for working with version 2 and 3 of
14 25 
     10X Genomics files. It simplifies importing by creating a class with
15 26 
     slots for version and group in the H5 file. Currently only H5 files are
Browse code

add validity to TENxFile

LiNk-NY authored on 24/05/2022 20:55:16
Showing 1 changed files
DESCRIPTION
History View file @ e88bfbc
... ... 
@@ -9,7 +9,7 @@ Authors@R:
9 9 
   )
10 10 
 Depends: R (>= 4.2.0)
11 11 
 Imports: BiocIO, BiocGenerics, MatrixGenerics, GenomeInfoDb,
12 
-  SingleCellMultiModal
12 
+  SingleCellMultiModal, S4Vectors
13 13 
 Description: The package exports methods for working with version 2 and 3 of
14 14 
     10X Genomics files. It simplifies importing by creating a class with
15 15 
     slots for version and group in the H5 file. Currently only H5 files are
Browse code

wip: add more data extensions and compressions

LiNk-NY authored on 24/05/2022 20:01:17
Showing 1 changed files
DESCRIPTION
History View file @ fed39f4
... ... 
@@ -7,8 +7,9 @@ Authors@R:
7 7 
     "Marcel", "Ramos", , "[email protected]",
8 8 
     c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 9 
   )
10 
-Imports: BiocIO
11 10 
 Depends: R (>= 4.2.0)
11 
+Imports: BiocIO, BiocGenerics, MatrixGenerics, GenomeInfoDb,
12 
+  SingleCellMultiModal
12 13 
 Description: The package exports methods for working with version 2 and 3 of
13 14 
     10X Genomics files. It simplifies importing by creating a class with
14 15 
     slots for version and group in the H5 file. Currently only H5 files are
Browse code

initial commit

LiNk-NY authored on 20/05/2022 20:39:38
Showing 1 changed files
DESCRIPTION
History View file @ d772031
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,18 @@
1 
+Package: TENxIO
2 
+Type: Package
3 
+Title: Import methods for 10X Genomics files
4 
+Version: 0.1.0
5 
+Authors@R:
6 
+  person(
7 
+    "Marcel", "Ramos", , "[email protected]",
8 
+    c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
9 
+  )
10 
+Imports: BiocIO
11 
+Depends: R (>= 4.2.0)
12 
+Description: The package exports methods for working with version 2 and 3 of
13 
+    10X Genomics files. It simplifies importing by creating a class with
14 
+    slots for version and group in the H5 file. Currently only H5 files are
15 
+    supported.
16 
+License: Artistic-2.0
17 
+Encoding: UTF-8
18 
+RoxygenNote: 7.1.2