... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.50.0 |
|
2 |
+Version: 1.51.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.8 |
|
2 |
+Version: 1.50.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,10 +1,10 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.7 |
|
2 |
+Version: 1.49.8 |
|
3 | 3 |
Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 |
- person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu"), |
|
7 |
+ person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablo.rodriguez.bio2@gmail.com"), |
|
8 | 8 |
person("Axel", "Klenk", role="ctb", email="axelvolker.klenk@upf.edu")) |
9 | 9 |
Depends: R (>= 3.5.0) |
10 | 10 |
Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.6 |
|
2 |
+Version: 1.49.7 |
|
3 | 3 |
Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.5 |
|
2 |
+Version: 1.49.6 |
|
3 | 3 |
Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,10 +1,11 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.4 |
|
2 |
+Version: 1.49.5 |
|
3 | 3 |
Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 |
- person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
|
7 |
+ person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu"), |
|
8 |
+ person("Axel", "Klenk", role="ctb", email="axelvolker.klenk@upf.edu")) |
|
8 | 9 |
Depends: R (>= 3.5.0) |
9 | 10 |
Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
10 | 11 |
Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, |
... | ... |
@@ -1,6 +1,6 @@ |
1 | 1 |
Package: GSVA |
2 | 2 |
Version: 1.49.4 |
3 |
-Title: Gene Set Variation Analysis for microarray and RNA-seq data |
|
3 |
+Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data |
|
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.3 |
|
2 |
+Version: 1.49.4 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.2 |
|
2 |
+Version: 1.49.3 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
85 ssgsea method parameter class and constructor
new_api sync to devel, 2nd attempt
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.1 |
|
2 |
+Version: 1.49.2 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.49.0 |
|
2 |
+Version: 1.49.1 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.48.0 |
|
2 |
+Version: 1.49.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.47.3 |
|
2 |
+Version: 1.48.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
merge in changes to devel
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.47.2 |
|
2 |
+Version: 1.47.3 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.47.1 |
|
2 |
+Version: 1.47.2 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.47.0 |
|
2 |
+Version: 1.47.1 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -18,5 +18,6 @@ License: GPL (>= 2) |
18 | 18 |
VignetteBuilder: knitr |
19 | 19 |
URL: https://github.com/rcastelo/GSVA |
20 | 20 |
BugReports: https://github.com/rcastelo/GSVA/issues |
21 |
-Encoding: latin1 |
|
21 |
+Encoding: UTF-8 |
|
22 | 22 |
biocViews: FunctionalGenomics, Microarray, RNASeq, Pathways, GeneSetEnrichment |
23 |
+RoxygenNote: 7.2.3 |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.46.0 |
|
2 |
+Version: 1.47.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.6 |
|
2 |
+Version: 1.46.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.5 |
|
2 |
+Version: 1.45.6 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
5 | 5 |
person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
... | ... |
@@ -1,8 +1,8 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.4 |
|
2 |
+Version: 1.45.5 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 |
-Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
|
5 |
- person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
|
4 |
+Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"), |
|
5 |
+ person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"), |
|
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 | 7 |
person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
8 | 8 |
Depends: R (>= 3.5.0) |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.3 |
|
2 |
+Version: 1.45.4 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -7,7 +7,7 @@ Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.gui |
7 | 7 |
person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
8 | 8 |
Depends: R (>= 3.5.0) |
9 | 9 |
Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
10 |
- Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
|
10 |
+ Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, |
|
11 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.2 |
|
2 |
+Version: 1.45.3 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.1 |
|
2 |
+Version: 1.45.2 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.45.0 |
|
2 |
+Version: 1.45.1 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.44.0 |
|
2 |
+Version: 1.45.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.43.1 |
|
2 |
+Version: 1.44.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.41.4 |
|
2 |
+Version: 1.41.5 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.42.0 |
|
2 |
+Version: 1.43.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.41.4 |
|
2 |
+Version: 1.42.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.41.3 |
|
2 |
+Version: 1.41.4 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.41.2 |
|
2 |
+Version: 1.41.3 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.41.1 |
|
2 |
+Version: 1.41.2 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.41.0 |
|
2 |
+Version: 1.41.1 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.40.0 |
|
2 |
+Version: 1.41.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.34 |
|
2 |
+Version: 1.40.0 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.33 |
|
2 |
+Version: 1.39.34 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.32 |
|
2 |
+Version: 1.39.33 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.30 |
|
2 |
+Version: 1.39.32 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.29 |
|
2 |
+Version: 1.39.30 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -11,7 +11,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
11 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
14 |
- org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, |
|
14 |
+ org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, |
|
15 | 15 |
data.table, plotly, future, promises, shinybusy, shinyjs |
16 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
17 | 17 |
License: GPL (>= 2) |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.28 |
|
2 |
+Version: 1.39.29 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.27 |
|
2 |
+Version: 1.39.28 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.26 |
|
2 |
+Version: 1.39.27 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.25 |
|
2 |
+Version: 1.39.26 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,9 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-<<<<<<< HEAD |
|
3 |
-Version: 1.39.24 |
|
4 |
-======= |
|
5 |
-Version: 1.39.23 |
|
6 |
->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d |
|
2 |
+Version: 1.39.25 |
|
7 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
8 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
9 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -15,13 +11,8 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
15 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
16 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
17 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
18 |
-<<<<<<< HEAD |
|
19 | 14 |
org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, |
20 |
- data.table, plotly, future, promises, shinybusy, org.Hs.eg.db |
|
21 |
-======= |
|
22 |
- genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
|
23 |
- plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db |
|
24 |
->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d |
|
15 |
+ data.table, plotly, future, promises, shinybusy, shinyjs |
|
25 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
26 | 17 |
License: GPL (>= 2) |
27 | 18 |
VignetteBuilder: knitr |
... | ... |
@@ -1,9 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-<<<<<<< HEAD |
|
3 | 2 |
Version: 1.39.24 |
4 |
-======= |
|
5 |
-Version: 1.39.23 |
|
6 |
->>>>>>> modules in shinyApp |
|
7 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
8 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
9 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -14,23 +10,9 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
14 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
15 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
16 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
17 |
-<<<<<<< HEAD |
|
18 |
-<<<<<<< HEAD |
|
19 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
20 | 14 |
org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, |
21 |
- data.table, plotly |
|
22 |
-======= |
|
23 |
-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
|
24 |
-======= |
|
25 |
-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
|
26 |
->>>>>>> modified imports in igsva() |
|
27 |
- genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
|
28 |
-<<<<<<< HEAD |
|
29 |
- plotly, shinyjs, future, promises, shinybusy |
|
30 |
->>>>>>> modules in shinyApp |
|
31 |
-======= |
|
32 |
- plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db |
|
33 |
->>>>>>> hide dwn and close btns |
|
15 |
+ data.table, plotly, future, promises, shinybusy, org.Hs.eg.db |
|
34 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
35 | 17 |
License: GPL (>= 2) |
36 | 18 |
VignetteBuilder: knitr |
... | ... |
@@ -15,11 +15,15 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
15 | 15 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
16 | 16 |
DelayedMatrixStats, HDF5Array, BiocSingular |
17 | 17 |
<<<<<<< HEAD |
18 |
+<<<<<<< HEAD |
|
18 | 19 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
19 | 20 |
org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, |
20 | 21 |
data.table, plotly |
21 | 22 |
======= |
22 | 23 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
24 |
+======= |
|
25 |
+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
|
26 |
+>>>>>>> modified imports in igsva() |
|
23 | 27 |
genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
24 | 28 |
<<<<<<< HEAD |
25 | 29 |
plotly, shinyjs, future, promises, shinybusy |
... | ... |
@@ -21,8 +21,12 @@ Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
21 | 21 |
======= |
22 | 22 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
23 | 23 |
genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
24 |
+<<<<<<< HEAD |
|
24 | 25 |
plotly, shinyjs, future, promises, shinybusy |
25 | 26 |
>>>>>>> modules in shinyApp |
27 |
+======= |
|
28 |
+ plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db |
|
29 |
+>>>>>>> hide dwn and close btns |
|
26 | 30 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
27 | 31 |
License: GPL (>= 2) |
28 | 32 |
VignetteBuilder: knitr |
... | ... |
@@ -1,5 +1,9 @@ |
1 | 1 |
Package: GSVA |
2 |
+<<<<<<< HEAD |
|
2 | 3 |
Version: 1.39.24 |
4 |
+======= |
|
5 |
+Version: 1.39.23 |
|
6 |
+>>>>>>> modules in shinyApp |
|
3 | 7 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 8 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 9 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -10,9 +14,15 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
10 | 14 |
Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
11 | 15 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 16 |
DelayedMatrixStats, HDF5Array, BiocSingular |
17 |
+<<<<<<< HEAD |
|
13 | 18 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
14 | 19 |
org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, |
15 | 20 |
data.table, plotly |
21 |
+======= |
|
22 |
+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
|
23 |
+ genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
|
24 |
+ plotly, shinyjs, future, promises, shinybusy |
|
25 |
+>>>>>>> modules in shinyApp |
|
16 | 26 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
17 | 27 |
License: GPL (>= 2) |
18 | 28 |
VignetteBuilder: knitr |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.23 |
|
2 |
+Version: 1.39.24 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -11,8 +11,8 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
11 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
14 |
- genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
|
15 |
- plotly |
|
14 |
+ org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, |
|
15 |
+ data.table, plotly |
|
16 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
17 | 17 |
License: GPL (>= 2) |
18 | 18 |
VignetteBuilder: knitr |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.22 |
|
2 |
+Version: 1.39.23 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -10,7 +10,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
11 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 |
-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
|
13 |
+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
|
14 | 14 |
genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
15 | 15 |
plotly |
16 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
... | ... |
@@ -10,7 +10,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
11 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 |
-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
|
13 |
+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, |
|
14 | 14 |
genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
15 | 15 |
plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db |
16 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
... | ... |
@@ -12,7 +12,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
14 | 14 |
genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
15 |
- plotly, shinyjs, future, promises, shinybusy |
|
15 |
+ plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db |
|
16 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
17 | 17 |
License: GPL (>= 2) |
18 | 18 |
VignetteBuilder: knitr |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.22 |
|
2 |
+Version: 1.39.23 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -12,7 +12,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 | 13 |
Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
14 | 14 |
genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
15 |
- plotly |
|
15 |
+ plotly, shinyjs, future, promises, shinybusy |
|
16 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
17 | 17 |
License: GPL (>= 2) |
18 | 18 |
VignetteBuilder: knitr |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.21 |
|
2 |
+Version: 1.39.22 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.20 |
|
2 |
+Version: 1.39.21 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.19 |
|
2 |
+Version: 1.39.20 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.18 |
|
2 |
+Version: 1.39.19 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,17 +1,18 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.17 |
|
2 |
+Version: 1.39.18 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 | 7 |
person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
8 | 8 |
Depends: R (>= 3.5.0) |
9 |
-Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, IRanges, |
|
9 |
+Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
|
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
11 | 11 |
BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
12 | 12 |
DelayedMatrixStats, HDF5Array, BiocSingular |
13 |
-Suggests: RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, genefilter, |
|
14 |
- edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, plotly |
|
13 |
+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, |
|
14 |
+ genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, |
|
15 |
+ plotly |
|
15 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
16 | 17 |
License: GPL (>= 2) |
17 | 18 |
VignetteBuilder: knitr |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.16 |
|
2 |
+Version: 1.39.17 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,24 +1,21 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.15 |
|
2 |
+Version: 1.39.16 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 | 7 |
person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
8 | 8 |
Depends: R (>= 3.5.0) |
9 |
-Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
|
10 |
- Biobase, SummarizedExperiment, GSEABase, Matrix, |
|
11 |
- parallel, BiocParallel, SingleCellExperiment, |
|
12 |
- sparseMatrixStats, DelayedArray, DelayedMatrixStats, |
|
13 |
- HDF5Array, BiocSingular |
|
14 |
-Suggests: |
|
15 |
- RUnit, BiocGenerics, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
|
16 |
- shiny, shinythemes, ggplot2, data.table, plotly |
|
9 |
+Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, IRanges, |
|
10 |
+ Biobase, SummarizedExperiment, GSEABase, Matrix, parallel, |
|
11 |
+ BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray, |
|
12 |
+ DelayedMatrixStats, HDF5Array, BiocSingular |
|
13 |
+Suggests: RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer, genefilter, |
|
14 |
+ edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, plotly |
|
17 | 15 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
18 | 16 |
License: GPL (>= 2) |
19 |
-LazyLoad: yes |
|
17 |
+VignetteBuilder: knitr |
|
20 | 18 |
URL: https://github.com/rcastelo/GSVA |
21 | 19 |
BugReports: https://github.com/rcastelo/GSVA/issues |
22 | 20 |
Encoding: latin1 |
23 |
-biocViews: Microarray, Pathways, GeneSetEnrichment |
|
24 |
-Config/testthat/edition: 3 |
|
21 |
+biocViews: FunctionalGenomics, Microarray, RNASeq, Pathways, GeneSetEnrichment |
... | ... |
@@ -1,14 +1,14 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.14 |
|
2 |
+Version: 1.39.15 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 | 7 |
person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
8 | 8 |
Depends: R (>= 3.5.0) |
9 |
-Imports: methods, stats, utils, graphics, S4Vectors, |
|
9 |
+Imports: methods, stats, utils, graphics, S4Vectors, IRanges, |
|
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, |
11 |
- parallel, BiocParallel, fastmatch, SingleCellExperiment, |
|
11 |
+ parallel, BiocParallel, SingleCellExperiment, |
|
12 | 12 |
sparseMatrixStats, DelayedArray, DelayedMatrixStats, |
13 | 13 |
HDF5Array, BiocSingular |
14 | 14 |
Suggests: |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.13 |
|
2 |
+Version: 1.39.14 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,18 +1,18 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.12 |
|
2 |
+Version: 1.39.13 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
6 | 6 |
person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"), |
7 | 7 |
person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu")) |
8 | 8 |
Depends: R (>= 3.5.0) |
9 |
-Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, |
|
9 |
+Imports: methods, stats, utils, graphics, S4Vectors, |
|
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, |
11 | 11 |
parallel, BiocParallel, fastmatch, SingleCellExperiment, |
12 | 12 |
sparseMatrixStats, DelayedArray, DelayedMatrixStats, |
13 | 13 |
HDF5Array, BiocSingular |
14 | 14 |
Suggests: |
15 |
- RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
|
15 |
+ RUnit, BiocGenerics, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
|
16 | 16 |
shiny, shinythemes, ggplot2, data.table, plotly |
17 | 17 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
18 | 18 |
License: GPL (>= 2) |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.11 |
|
2 |
+Version: 1.39.12 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.12 |
|
2 |
+Version: 1.39.11 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.11 |
|
2 |
+Version: 1.39.12 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -10,9 +10,10 @@ Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, |
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, |
11 | 11 |
parallel, BiocParallel, fastmatch, SingleCellExperiment, |
12 | 12 |
sparseMatrixStats, DelayedArray, DelayedMatrixStats, |
13 |
- HDF5Array |
|
14 |
-Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
|
15 |
- shiny, shinythemes, ggplot2, data.table, plotly |
|
13 |
+ HDF5Array, BiocSingular |
|
14 |
+Suggests: |
|
15 |
+ RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
|
16 |
+ shiny, shinythemes, ggplot2, data.table, plotly |
|
16 | 17 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
17 | 18 |
License: GPL (>= 2) |
18 | 19 |
LazyLoad: yes |
... | ... |
@@ -20,3 +21,4 @@ URL: https://github.com/rcastelo/GSVA |
20 | 21 |
BugReports: https://github.com/rcastelo/GSVA/issues |
21 | 22 |
Encoding: latin1 |
22 | 23 |
biocViews: Microarray, Pathways, GeneSetEnrichment |
24 |
+Config/testthat/edition: 3 |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.10 |
|
2 |
+Version: 1.39.11 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.9 |
|
2 |
+Version: 1.39.10 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.8 |
|
2 |
+Version: 1.39.9 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.9 |
|
2 |
+Version: 1.39.8 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.8 |
|
2 |
+Version: 1.39.9 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.7 |
|
2 |
+Version: 1.39.8 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -8,8 +8,9 @@ Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.gui |
8 | 8 |
Depends: R (>= 3.5.0) |
9 | 9 |
Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, |
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, |
11 |
- parallel, BiocParallel, fastmatch, SingleCellExperiment, |
|
12 |
- BiocSingular, sparseMatrixStats |
|
11 |
+ parallel, BiocParallel, fastmatch, SingleCellExperiment, |
|
12 |
+ sparseMatrixStats, DelayedArray, DelayedMatrixStats, |
|
13 |
+ HDF5Array |
|
13 | 14 |
Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
14 | 15 |
shiny, shinythemes, ggplot2, data.table, plotly |
15 | 16 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.6 |
|
2 |
+Version: 1.39.7 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -9,7 +9,7 @@ Depends: R (>= 3.5.0) |
9 | 9 |
Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, |
10 | 10 |
Biobase, SummarizedExperiment, GSEABase, Matrix, |
11 | 11 |
parallel, BiocParallel, fastmatch, SingleCellExperiment, |
12 |
- BiocSingular |
|
12 |
+ BiocSingular, sparseMatrixStats |
|
13 | 13 |
Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata, |
14 | 14 |
shiny, shinythemes, ggplot2, data.table, plotly |
15 | 15 |
Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.5 |
|
2 |
+Version: 1.39.6 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
Package: GSVA |
2 |
-Version: 1.39.4 |
|
2 |
+Version: 1.39.5 |
|
3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"), |
5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"), |
... | ... |
@@ -8,7 +8,8 @@ Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.gui |
8 |