1. GSVA
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:05:54
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 Package: GSVA
2 
-Version: 1.46.0
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+Version: 1.47.0
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 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"),
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bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:05:54
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1 1 
 Package: GSVA
2 
-Version: 1.45.6
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+Version: 1.46.0
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 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"),
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Updated NEWS file

Robert Castelo authored on 31/10/2022 15:48:30
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 Package: GSVA
2 
-Version: 1.45.5
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+Version: 1.45.6
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
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Switching official maintainer to Robert Castelo

Robert Castelo authored on 20/09/2022 18:15:24
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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"),
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-             person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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+Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"),
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+             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)
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Enforcing minimum version of the upstream dependency Matrix 1.5-0

Robert Castelo authored on 20/09/2022 05:19:18
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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"),
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@@ -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,
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+         Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel,
11 11 
          BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray,
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          DelayedMatrixStats, HDF5Array, BiocSingular
13 13 
 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
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Changed coercions to dgCMatrix to go via virtual classes to comply with latest updates in Matrix version 1.4-2

Robert Castelo authored on 06/09/2022 14:25:29
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 Package: GSVA
2 
-Version: 1.45.2
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+Version: 1.45.3
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
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Bugfix when input is a SummarizedExperiment and assays contain a data.frame instead of a matrix

[rcastelo] authored on 09/06/2022 14:21:42
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 Package: GSVA
2 
-Version: 1.45.1
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+Version: 1.45.2
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 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"),
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Bugfix when using ssgsea with one single sample in the input expression data matrix. Reported by Christopher Eeles at https://github.com/rcastelo/GSVA/issues/61

Robert Castelo authored on 31/05/2022 07:32:44
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 Package: GSVA
2 
-Version: 1.45.0
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+Version: 1.45.1
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 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"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:07:47
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 Package: GSVA
2 
-Version: 1.44.0
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+Version: 1.45.0
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 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"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:07:47
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1 1 
 Package: GSVA
2 
-Version: 1.43.1
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+Version: 1.44.0
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 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"),
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Resolved conflict on package version in DESCRIPTION file

Robert Castelo authored on 19/11/2021 11:38:00
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changing function viewReduce for gridReduce from DelayedArray

pablo-rodr-bio2 authored on 18/11/2021 08:36:13
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1 1 
 Package: GSVA
2 
-Version: 1.41.4
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+Version: 1.41.5
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 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"),
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:59:07
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1 1 
 Package: GSVA
2 
-Version: 1.42.0
2 
+Version: 1.43.0
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 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"),
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bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:59:07
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 Package: GSVA
2 
-Version: 1.41.4
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+Version: 1.42.0
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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Fixed unit test and updated NEWS file

[rcastelo] authored on 25/10/2021 15:10:55
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1 1 
 Package: GSVA
2 
-Version: 1.41.3
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+Version: 1.41.4
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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remove CITATION.cff file

Robert Castelo authored on 28/07/2021 15:38:41
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 Package: GSVA
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-Version: 1.41.2
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+Version: 1.41.3
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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Added CITATION.cff file

Robert Castelo authored on 28/07/2021 12:03:18
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1 1 
 Package: GSVA
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-Version: 1.41.1
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+Version: 1.41.2
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
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Bugfix to enforce DelayedMatrixStats::rowSds(), with matrixStats::rowSds() behind the scenes, giving an exact zero where base sd() would also give an exact zero. See https://github.com/rcastelo/GSVA/issues/54 and https://github.com/HenrikBengtsson/matrixStats/issues/204

[rcastelo] authored on 03/06/2021 15:42:11
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1 1 
 Package: GSVA
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-Version: 1.41.0
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+Version: 1.41.1
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 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"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:48:35
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1 1 
 Package: GSVA
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-Version: 1.40.0
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+Version: 1.41.0
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:48:35
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1 1 
 Package: GSVA
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-Version: 1.39.34
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+Version: 1.40.0
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 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"),
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Updated vignette, documentation and NEWS file, corrected some messages and warnings.

Robert Castelo authored on 18/05/2021 21:31:15
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 Package: GSVA
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-Version: 1.39.33
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+Version: 1.39.34
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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take out shinythemes from global

pablo-rodr-bio2 authored on 18/05/2021 10:28:35
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1 1 
 Package: GSVA
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-Version: 1.39.32
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+Version: 1.39.33
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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new css changes in dashboard

pablo-rodr-bio2 authored on 17/05/2021 17:29:04
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 Package: GSVA
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-Version: 1.39.30
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+Version: 1.39.32
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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beautifying UI

pablo-rodr-bio2 authored on 14/05/2021 09:37:52
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 Package: GSVA
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-Version: 1.39.29
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+Version: 1.39.30
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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added css for title and btns

pablo-rodr-bio2 authored on 13/05/2021 11:26:15
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@@ -11,7 +11,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges,
11 11 
          BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray,
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          DelayedMatrixStats, HDF5Array, BiocSingular
13 13 
 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
14 
-          org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2,
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+          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)
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changed version

pablo-rodr-bio2 authored on 11/05/2021 15:31:56
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1 1 
 Package: GSVA
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-Version: 1.39.28
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+Version: 1.39.29
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
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removed filterFeatureSparse()

pablo-rodr-bio2 authored on 03/05/2021 12:24:35
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 Package: GSVA
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-Version: 1.39.27
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+Version: 1.39.28
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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added minor css to title

pablo-rodr-bio2 authored on 30/04/2021 10:26:32
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 Package: GSVA
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-Version: 1.39.26
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+Version: 1.39.27
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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method in x label, args change with method

pablo-rodr-bio2 authored on 29/04/2021 17:41:04
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 Package: GSVA
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-Version: 1.39.25
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+Version: 1.39.26
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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modularizing and fixing bugs

pablo-rodr-bio2 authored on 26/04/2021 10:56:26
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 Package: GSVA
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-<<<<<<< HEAD
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-Version: 1.39.24
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-=======
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-Version: 1.39.23
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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+Version: 1.39.25
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 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"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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@@ -15,13 +11,8 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges,
15 11 
          BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray,
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          DelayedMatrixStats, HDF5Array, BiocSingular
17 13 
 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
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-<<<<<<< HEAD
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           org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2,
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-          data.table, plotly, future, promises, shinybusy, org.Hs.eg.db
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-=======
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-          genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table,
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-          plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db
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->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d
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+          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
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rebased

pablo-rodr-bio2 authored on 22/04/2021 22:05:25
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rebased

pablo-rodr-bio2 authored on 22/04/2021 16:03:37
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 Package: GSVA
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-<<<<<<< HEAD
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 Version: 1.39.24
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-=======
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-Version: 1.39.23
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->>>>>>> modules in shinyApp
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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@@ -14,23 +10,9 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges,
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          Biobase, SummarizedExperiment, GSEABase, Matrix, parallel,
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          BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray,
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          DelayedMatrixStats, HDF5Array, BiocSingular
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-<<<<<<< HEAD
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-<<<<<<< HEAD
19 13 
 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
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           org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2,
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-          data.table, plotly
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-=======
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-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer,
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-=======
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-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
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->>>>>>> modified imports in igsva()
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-          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
Browse code

modified imports in igsva()

pablo-rodr-bio2 authored on 19/04/2021 11:20:20
Showing 1 changed files
DESCRIPTION
History View file @ 055f2806
... ... 
@@ -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
Browse code

hide dwn and close btns

pablo-rodr-bio2 authored on 13/04/2021 17:00:38
Showing 1 changed files
DESCRIPTION
History View file @ e32501d2
... ... 
@@ -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
Browse code

modules in shinyApp

pablo-rodr-bio2 authored on 12/04/2021 19:41:34
Showing 1 changed files
DESCRIPTION
History View file @ ca2b622a
... ... 
@@ -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
Browse code

Add org.Hs.eg.db to suggests.

[rcastelo] authored on 21/04/2021 13:20:31
Showing 1 changed files
DESCRIPTION
History View file @ 8a635107
... ... 
@@ -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
Browse code

Replaced markdown by rmarkdown in suggests.

[rcastelo] authored on 21/04/2021 11:57:02
Showing 1 changed files
DESCRIPTION
History View file @ 61184714
... ... 
@@ -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.
Browse code

modified imports in igsva()

pablo-rodr-bio2 authored on 19/04/2021 11:20:20
Showing 1 changed files
DESCRIPTION
History View file @ 464936e4
... ... 
@@ -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.
Browse code

hide dwn and close btns

pablo-rodr-bio2 authored on 13/04/2021 17:00:38
Showing 1 changed files
DESCRIPTION
History View file @ 98c1bac6
... ... 
@@ -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
Browse code

modules in shinyApp

pablo-rodr-bio2 authored on 12/04/2021 19:41:34
Showing 1 changed files
DESCRIPTION
History View file @ f2b69b61
... ... 
@@ -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
Browse code

Updated vignette.

Robert Castelo authored on 30/03/2021 20:12:25
Showing 1 changed files
DESCRIPTION
History View file @ 53a9b5e5
... ... 
@@ -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"),
Browse code

Updated vignette and README.

Robert Castelo authored on 30/03/2021 17:49:45
Showing 1 changed files
DESCRIPTION
History View file @ bbb4b100
... ... 
@@ -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"),
Browse code

Updated vignette and added GHA.

Robert Castelo authored on 30/03/2021 17:42:22
Showing 1 changed files
DESCRIPTION
History View file @ 49edead0
... ... 
@@ -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"),
Browse code

Updated README.

Robert Castelo authored on 30/03/2021 11:22:06
Showing 1 changed files
DESCRIPTION
History View file @ a16b0ac5
... ... 
@@ -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"),
Browse code

Some fixes removing the dependency of fastmatch and other minor issues.

[rcastelo] authored on 03/03/2021 11:07:14
Showing 1 changed files
DESCRIPTION
History View file @ 98d91f50
... ... 
@@ -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
Browse code

Fixed gsva() method for signature matrix and GeneSetCollection.

Robert Castelo authored on 09/02/2021 12:11:44
Showing 1 changed files
DESCRIPTION
History View file @ d5ee4c65
... ... 
@@ -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"),
Browse code

Started updating the vignette.

Robert Castelo authored on 05/02/2021 18:07:16
Showing 1 changed files
DESCRIPTION
History View file @ b77eaecf
... ... 
@@ -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
Browse code

Replaced fastmatch::fmatch() by IRanges::match,CharacterList-method after disscussion at https://github.com/rcastelo/GSVA/issues/39

Robert Castelo authored on 03/02/2021 16:09:12
Showing 1 changed files
DESCRIPTION
History View file @ 0093798f
... ... 
@@ -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:
Browse code

Fixed wrong call to .mapGeneSetsToFeatures when gene sets are given in a GeneSetCollection object.

Robert Castelo authored on 03/02/2021 12:32:10
Showing 1 changed files
DESCRIPTION
History View file @ 6040bc0e
... ... 
@@ -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"),
Browse code

Fixing a bug in delayed zscore method and getting back tests

pablo-rodr-bio2 authored on 25/01/2021 17:51:59
Showing 1 changed files
DESCRIPTION
History View file @ 1a9a4353
... ... 
@@ -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)
Browse code

Fixed call to fastmatch::fmatch() to avoid that this call modifies rownames of input expression matrices. Use this opportunity to factor out relevant code.

Robert Castelo authored on 22/01/2021 11:27:10
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1 1 
 Package: GSVA
2 
-Version: 1.39.11
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+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"),
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adding runRandomSVD() to plageDelayed method for better use of on-disk backend

pablo-rodr-bio2 authored on 11/01/2021 17:31:01
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@@ -1,5 +1,5 @@
1 1 
 Package: GSVA
2 
-Version: 1.39.12
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+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"),
Browse code

adding runRandomSVD() to plageDelayed method for better use of on-disk backend

pablo-rodr-bio2 authored on 11/01/2021 11:22:49
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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"),
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@@ -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
Browse code

added ssgsea method for DelayedArray

pablo-rodr-bio2 authored on 15/12/2020 13:14:39
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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"),
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added delayed support for zscore method

pablo-rodr-bio2 authored on 02/12/2020 17:31:38
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 Package: GSVA
2 
-Version: 1.39.9
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+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"),
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Bumped version.

Robert Castelo authored on 26/11/2020 12:22:45
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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"),
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Removed .Rhistory, added .gitignore, decrease version in DESCRIPTION to have consecutive versions.

Robert Castelo authored on 26/11/2020 12:21:47
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1 1 
 Package: GSVA
2 
-Version: 1.39.9
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+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"),
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added delayed support for plage method

pablo-rodr-bio2 authored on 24/11/2020 16:56:20
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1 1 
 Package: GSVA
2 
-Version: 1.39.8
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 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"),
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added hdf5 support for plage method

pablo-rodr-bio2 authored on 20/11/2020 18:38:41
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@@ -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"),
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@@ -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,
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-         BiocSingular, sparseMatrixStats
11 
+         parallel, BiocParallel, fastmatch, SingleCellExperiment,
12 
+         sparseMatrixStats, DelayedArray, DelayedMatrixStats,
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+         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.
Browse code

adding sparse support to method ssgsea

pablo-rodr-bio2 authored on 13/11/2020 12:45:26
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@@ -1,5 +1,5 @@
1 1 
 Package: GSVA
2 
-Version: 1.39.6
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+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"),
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@@ -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,
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-         BiocSingular
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+         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.
Browse code

adding sparse support to zscore method

pablo-rodr-bio2 authored on 11/11/2020 19:13:24
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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"),
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adding sparse support to method plage

pablo-rodr-bio2 authored on 10/11/2020 11:04:28
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@@ -1,5 +1,5 @@
1 1 
 Package: GSVA
2 
-Version: 1.39.4
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+Version: 1.39.5
3 3 
 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
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adding dgCMatrix support to method plage

pablo-rodr-bio2 authored on 09/11/2020 11:11:55
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@@ -8,7 +8,8 @@ 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
11 
+         parallel, BiocParallel, fastmatch, SingleCellExperiment,
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+         BiocSingular
12 13 
 Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata,
13 14 
           shiny, shinythemes, ggplot2, data.table, plotly
14 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.
Browse code

Fixed unit test.

[rcastelo] authored on 05/11/2020 16:37:55
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1 1 
 Package: GSVA
2 
-Version: 1.39.3
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+Version: 1.39.4
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"),
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Added unit test for dgCMatrix data container.

[rcastelo] authored on 05/11/2020 16:20:41
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 Package: GSVA
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-Version: 1.39.2
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+Version: 1.39.3
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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adding dgCMatrix/list support

pablo-rodr-bio2 authored on 02/11/2020 18:21:42
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 Package: GSVA
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-Version: 1.39.1
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+Version: 1.39.2
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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adding dgCMatrix/list support

pablo-rodr-bio2 authored on 02/11/2020 18:20:08
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@@ -7,7 +7,7 @@ Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.gui
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              person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu"))
8 8 
 Depends: R (>= 3.5.0)
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 Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors,
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-         Biobase, SummarizedExperiment, GSEABase,
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+         Biobase, SummarizedExperiment, GSEABase, Matrix,
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          parallel, BiocParallel, fastmatch, SingleCellExperiment
12 12 
 Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata,
13 13 
           shiny, shinythemes, ggplot2, data.table, plotly
Browse code

Fixed file encoding for man/gsva.Rd.

[rcastelo] authored on 02/11/2020 14:49:46
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1 1 
 Package: GSVA
2 
-Version: 1.39.0
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+Version: 1.39.1
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
Browse code

Merge branch 'singleCell-support' of https://github.com/pablo-rodr-bio2/GSVA into pablo-rodr-bio2-singleCell-support

[rcastelo] authored on 02/11/2020 11:22:46
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adding SingleCellExperiment support

pablo-rodr-bio2 authored on 29/10/2020 11:43:14
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@@ -8,7 +8,7 @@ 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,
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-         parallel, BiocParallel, fastmatch
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+         parallel, BiocParallel, fastmatch, SingleCellExperiment
12 12 
 Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata,
13 13 
           shiny, shinythemes, ggplot2, data.table, plotly
14 14 
 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.
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:41:30
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 Package: GSVA
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+Version: 1.39.0
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:41:30
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 Package: GSVA
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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Fix mapping to features for which expression data is available.

[rcastelo] authored on 07/10/2020 08:11:30
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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Removed parallelization throughout gene sets in the internal zscore() function. Moved shiny app dependencies to suggests.

Robert Castelo authored on 01/09/2020 17:18:39
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1 1 
 Package: GSVA
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-Version: 1.37.3
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+Version: 1.37.4
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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 Depends: R (>= 3.5.0)
9 9 
 Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors,
10 10 
          Biobase, SummarizedExperiment, GSEABase,
11 
-         parallel, BiocParallel, shiny, shinythemes,
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-         fastmatch
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+         parallel, BiocParallel, fastmatch
13 12 
 Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata,
14 
-          data.table, plotly
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+          shiny, shinythemes, ggplot2, data.table, plotly
15 14 
 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 15 
 License: GPL (>= 2)
17 16 
 LazyLoad: yes
Browse code

Bump version.

Robert Castelo authored on 17/06/2020 10:48:16
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 Package: GSVA
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 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"),
Browse code

Bugfix when input data is a SummarizedExperiment. Corresponding unit test added.

Robert Castelo authored on 29/05/2020 15:47:09
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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Bump version.

Robert Castelo authored on 27/05/2020 16:47:38
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1 1 
 Package: GSVA
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-Version: 1.37.0
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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-             person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"))
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+             person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"),
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+             person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu"))
7 8 
 Depends: R (>= 3.5.0)
8 9 
 Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors,
9 10 
          Biobase, SummarizedExperiment, GSEABase,
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          parallel, BiocParallel, shiny, shinythemes,
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          fastmatch
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-Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata
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+Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata,
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+          data.table, plotly
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 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.
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 License: GPL (>= 2)
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 LazyLoad: yes
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:25:37
Showing 1 changed files
DESCRIPTION
History View file @ fa96bc97
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 Package: GSVA
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-Version: 1.36.0
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+Version: 1.37.0
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:25:36
Showing 1 changed files
DESCRIPTION
History View file @ 2e12e87f
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@@ -1,5 +1,5 @@
1 1 
 Package: GSVA
2 
-Version: 1.35.7
2 
+Version: 1.36.0
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),