1. SpatialDecon
  2. NAMESPACE
Browse code

logNormReg update with updated test data

Maddy Griswold authored on 09/08/2022 20:32:26
Showing 1 changed files
NAMESPACE
History View file @ 97741d0
... ... 
@@ -28,6 +28,7 @@ importFrom(graphics,lines)
28 28 
 importFrom(graphics,plot)
29 29 
 importFrom(graphics,polygon)
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 importFrom(graphics,text)
31 
+importFrom(logNormReg,lognlm)
31 32 
 importFrom(methods,is)
32 33 
 importFrom(repmis,source_data)
33 34 
 importFrom(stats,cor)
Browse code

update documentation after removing logNormReg

Maddy Griswold authored on 02/11/2021 20:18:05
Showing 1 changed files
NAMESPACE
History View file @ 20454d3
... ... 
@@ -15,7 +15,6 @@ exportMethods(runMergeTumorIntoX)
15 15 
 exportMethods(runReverseDecon)
16 16 
 exportMethods(runspatialdecon)
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 import(graphics)
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-import(logNormReg)
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 import(stats)
20 19 
 import(utils)
21 20 
 importClassesFrom(GeomxTools,NanoStringGeoMxSet)
... ... 
@@ -29,7 +28,6 @@ importFrom(graphics,lines)
29 28 
 importFrom(graphics,plot)
30 29 
 importFrom(graphics,polygon)
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 importFrom(graphics,text)
32 
-importFrom(logNormReg,lognlm)
33 31 
 importFrom(methods,is)
34 32 
 importFrom(repmis,source_data)
35 33 
 importFrom(stats,cor)
Browse code

BiocCheck and devtools::check updates

Maddy Griswold authored on 11/10/2021 21:58:36
Showing 1 changed files
NAMESPACE
History View file @ 3b0b32e
... ... 
@@ -8,13 +8,16 @@ export(download_profile_matrix)
8 8 
 export(florets)
9 9 
 export(mergeTumorIntoX)
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 export(reverseDecon)
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-export(runCollapseCellTypes)
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 export(runErrorModel)
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-export(runMergeTumorIntoX)
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-export(runReverseDecon)
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 export(spatialdecon)
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+exportMethods(runCollapseCellTypes)
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+exportMethods(runMergeTumorIntoX)
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+exportMethods(runReverseDecon)
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 exportMethods(runspatialdecon)
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+import(graphics)
17 18 
 import(logNormReg)
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+import(stats)
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+import(utils)
18 21 
 importClassesFrom(GeomxTools,NanoStringGeoMxSet)
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 importFrom(Biobase,assayData)
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 importFrom(SeuratObject,GetAssayData)
... ... 
@@ -27,6 +30,7 @@ importFrom(graphics,plot)
27 30 
 importFrom(graphics,polygon)
28 31 
 importFrom(graphics,text)
29 32 
 importFrom(logNormReg,lognlm)
33 
+importFrom(methods,is)
30 34 
 importFrom(repmis,source_data)
31 35 
 importFrom(stats,cor)
32 36 
 importFrom(stats,cutree)
Browse code

GeomxTools wrapper: functions, mans, tests, vignettes

Maddy Griswold authored on 27/09/2021 18:34:06
Showing 1 changed files
NAMESPACE
History View file @ 1610c2f
... ... 
@@ -8,6 +8,7 @@ export(download_profile_matrix)
8 8 
 export(florets)
9 9 
 export(mergeTumorIntoX)
10 10 
 export(reverseDecon)
11 
+export(runCollapseCellTypes)
11 12 
 export(runErrorModel)
12 13 
 export(runMergeTumorIntoX)
13 14 
 export(runReverseDecon)
Browse code

merge all branches and update tests

Maddy Griswold authored on 22/09/2021 23:31:09
Showing 1 changed files
NAMESPACE
History View file @ b3aa953
... ... 
@@ -9,9 +9,13 @@ export(florets)
9 9 
 export(mergeTumorIntoX)
10 10 
 export(reverseDecon)
11 11 
 export(runErrorModel)
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+export(runMergeTumorIntoX)
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+export(runReverseDecon)
12 14 
 export(spatialdecon)
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 exportMethods(runspatialdecon)
14 16 
 import(logNormReg)
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+importClassesFrom(GeomxTools,NanoStringGeoMxSet)
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+importFrom(Biobase,assayData)
15 19 
 importFrom(SeuratObject,GetAssayData)
16 20 
 importFrom(grDevices,colors)
17 21 
 importFrom(graphics,barplot)
Browse code

Merge branch 'create_profile_matrix' into v1.3_release

Maddy Griswold authored on 22/09/2021 15:55:47
Showing 0 changed files
Browse code

Added create_profile_matrix function

Created minimal viable function to create custom profile matrix from single cell data. Users must provide read in count matrix rather than files.

Maddy Griswold authored on 10/09/2021 18:11:51
Showing 1 changed files
NAMESPACE
History View file @ 12832d9
... ... 
@@ -2,6 +2,7 @@
2 2
3 3 
 export(TIL_barplot)
4 4 
 export(collapseCellTypes)
5 
+export(create_profile_matrix)
5 6 
 export(derive_GeoMx_background)
6 7 
 export(download_profile_matrix)
7 8 
 export(florets)
Browse code

docs for runErrorModel

Patrick Danaher authored on 17/08/2021 22:25:11
Showing 1 changed files
NAMESPACE
History View file @ ae4fb04
... ... 
@@ -7,6 +7,7 @@ export(download_profile_matrix)
7 7 
 export(florets)
8 8 
 export(mergeTumorIntoX)
9 9 
 export(reverseDecon)
10 
+export(runErrorModel)
10 11 
 export(spatialdecon)
11 12 
 exportMethods(runspatialdecon)
12 13 
 import(logNormReg)
Browse code

Merge branch 'revisions-for-journal' into updateDownloadMatrix

Patrick Danaher authored on 10/08/2021 22:29:47 • GitHub committed on 10/08/2021 22:29:47
Showing 0 changed files
Browse code

download new matrices

links to matrices will need to be updated when they are merged with master

Maddy Griswold authored on 10/08/2021 19:35:39
Showing 1 changed files
NAMESPACE
History View file @ 4730db8
... ... 
@@ -18,6 +18,7 @@ importFrom(graphics,plot)
18 18 
 importFrom(graphics,polygon)
19 19 
 importFrom(graphics,text)
20 20 
 importFrom(logNormReg,lognlm)
21 
+importFrom(repmis,source_data)
21 22 
 importFrom(stats,cor)
22 23 
 importFrom(stats,cutree)
23 24 
 importFrom(stats,dist)
Browse code

start building geomxset method

Patrick Danaher authored on 30/04/2021 19:49:20
Showing 1 changed files
NAMESPACE
History View file @ 2cca309
... ... 
@@ -8,7 +8,9 @@ export(florets)
8 8 
 export(mergeTumorIntoX)
9 9 
 export(reverseDecon)
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 export(spatialdecon)
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+exportMethods(runspatialdecon)
11 12 
 import(logNormReg)
13 
+importFrom(SeuratObject,GetAssayData)
12 14 
 importFrom(grDevices,colors)
13 15 
 importFrom(graphics,barplot)
14 16 
 importFrom(graphics,frame)
Browse code

pnorm instead of pt

Patrick Danaher authored on 20/04/2021 00:10:57
Showing 1 changed files
NAMESPACE
History View file @ 3150d8e
... ... 
@@ -23,7 +23,7 @@ importFrom(stats,cutree)
23 23 
 importFrom(stats,dist)
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 importFrom(stats,hclust)
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 importFrom(stats,lm)
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-importFrom(stats,pt)
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+importFrom(stats,pnorm)
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 importFrom(stats,quantile)
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 importFrom(stats,sd)
29 29 
 importFrom(utils,data)
Browse code

updates for bioC

- lazyload = FALSE (causes some check() warnings and notes)
- @keywords internal added
- fixed docs for mini_geomx_dataset
- vignette toc added
- vignette installation instructions added
- @importfrom's added

Patrick Danaher authored on 16/10/2020 22:38:29
Showing 1 changed files
NAMESPACE
History View file @ 8629379
... ... 
@@ -9,3 +9,22 @@ export(mergeTumorIntoX)
9 9 
 export(reverseDecon)
10 10 
 export(spatialdecon)
11 11 
 import(logNormReg)
12 
+importFrom(grDevices,colors)
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+importFrom(graphics,barplot)
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+importFrom(graphics,frame)
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+importFrom(graphics,legend)
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+importFrom(graphics,lines)
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+importFrom(graphics,plot)
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+importFrom(graphics,polygon)
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+importFrom(graphics,text)
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+importFrom(logNormReg,lognlm)
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+importFrom(stats,cor)
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+importFrom(stats,cutree)
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+importFrom(stats,dist)
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+importFrom(stats,hclust)
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+importFrom(stats,lm)
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+importFrom(stats,pt)
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+importFrom(stats,quantile)
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+importFrom(stats,sd)
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+importFrom(utils,data)
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+importFrom(utils,read.csv)
Browse code

more bioc formatting

Patrick Danaher authored on 24/09/2020 06:00:20
Showing 1 changed files
NAMESPACE
History View file @ 237b158
... ... 
@@ -1,11 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(TIL_barplot)
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-export(algorithm2)
5 4 
 export(collapseCellTypes)
6 5 
 export(derive_GeoMx_background)
7 6 
 export(download_profile_matrix)
8 
-export(flagOutliers)
9 7 
 export(florets)
10 8 
 export(mergeTumorIntoX)
11 9 
 export(reverseDecon)
Browse code

rename derive_GeoMx_background

patrickjdanaher authored on 28/07/2020 16:43:47
Showing 1 changed files
NAMESPACE
History View file @ 2797e44
... ... 
@@ -3,7 +3,7 @@
3 3 
 export(TIL_barplot)
4 4 
 export(algorithm2)
5 5 
 export(collapseCellTypes)
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-export(derive_GeoMx_background_at_normalized_scale)
6 
+export(derive_GeoMx_background)
7 7 
 export(download_profile_matrix)
8 8 
 export(flagOutliers)
9 9 
 export(florets)
Browse code

add convertcelltypes and update vignette

Patrick Danaher authored on 17/07/2020 22:59:21
Showing 1 changed files
NAMESPACE
History View file @ 79cb985
... ... 
@@ -2,8 +2,7 @@
2 2
3 3 
 export(TIL_barplot)
4 4 
 export(algorithm2)
5 
-export(convertCellTypes)
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-export(deriveWeights)
5 
+export(collapseCellTypes)
7 6 
 export(derive_GeoMx_background_at_normalized_scale)
8 7 
 export(download_profile_matrix)
9 8 
 export(flagOutliers)
Browse code

rename insitusort -> spatialdecon

Patrick Danaher authored on 17/07/2020 19:03:44
Showing 1 changed files
NAMESPACE
History View file @ 06f301c
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,14 @@
1 
+# Generated by roxygen2: do not edit by hand
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+
3 
+export(TIL_barplot)
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+export(algorithm2)
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+export(convertCellTypes)
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+export(deriveWeights)
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+export(derive_GeoMx_background_at_normalized_scale)
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+export(download_profile_matrix)
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+export(flagOutliers)
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+export(florets)
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+export(mergeTumorIntoX)
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+export(reverseDecon)
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+export(spatialdecon)
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+import(logNormReg)