1. GSVA
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 13:46:46
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1 1 
 Package: GSVA
2 
-Version: 1.50.0
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+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"),
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bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 13:46:46
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1 1 
 Package: GSVA
2 
-Version: 1.49.8
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+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"),
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Updated NEWS file

Robert Castelo authored on 20/10/2023 16:48:28
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1 1 
 Package: GSVA
2 
-Version: 1.49.7
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+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"),
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-             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,
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unify handling and add checking of new arguments 'annotation' and 'assay'. move some utility functions to R/utils.R (!)

Axel Klenk authored on 19/10/2023 20:51:13
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 Package: GSVA
2 
-Version: 1.49.6
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+Version: 1.49.7
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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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add show() methods for parameter objects that re-use components' show where appropriate and override them otherwise

Axel Klenk authored on 09/10/2023 15:07:45
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 Package: GSVA
2 
-Version: 1.49.5
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+Version: 1.49.6
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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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New API first version, more documentation and unit tests to be added; existing code using the 'old' API should continue work.

Axel Klenk authored on 15/09/2023 17:41:39
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1 1 
 Package: GSVA
2 
-Version: 1.49.4
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+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"),
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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"))
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+             person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu"),
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+             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,
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fix --as-cran NOTE on using title case in the package title :-)

Axel Klenk authored on 01/08/2023 17:26:58
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 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"),
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merge in a couple of unrelated fixes from devel

Axel Klenk authored on 01/08/2023 15:03:08
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Merging PR https://github.com/rcastelo/GSVA/pull/99 that improves the parallelization of the zscore method

Robert Castelo authored on 28/07/2023 17:30:29
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 Package: GSVA
2 
-Version: 1.49.3
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+Version: 1.49.4
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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"),
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              person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"),
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Fixed bug on C method registration and a couple of --as-cran notes

Robert Castelo authored on 27/07/2023 17:19:23
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 Package: GSVA
2 
-Version: 1.49.2
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+Version: 1.49.3
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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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Merge pull request #95 from rcastelo/85-ssgsea-method-parameter-class-and-constructor

85 ssgsea method parameter class and constructor

Axel Klenk authored on 14/07/2023 15:16:32 • GitHub committed on 14/07/2023 15:16:32
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finalize ssGSEA; remove allGenerics.R and, on second thoughts, make ssgseaParam getters *functions* instead of methods

Axel Klenk authored on 14/07/2023 14:59:31
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@@ -20,4 +20,5 @@ URL: https://github.com/rcastelo/GSVA
20 20 
 BugReports: https://github.com/rcastelo/GSVA/issues
21 21 
 Encoding: UTF-8
22 22 
 biocViews: FunctionalGenomics, Microarray, RNASeq, Pathways, GeneSetEnrichment
23 
+Roxygen: list(markdown = TRUE)
23 24 
 RoxygenNote: 7.2.3
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Merge pull request #94 from rcastelo/devel

new_api sync to devel, 2nd attempt

Axel Klenk authored on 10/07/2023 11:17:17 • GitHub committed on 10/07/2023 11:17:17
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Bugfix in the call to C code by the GSVA algorithm to enable working with long vectors.

Robert Castelo authored on 23/06/2023 16:47:38
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 Package: GSVA
2 
-Version: 1.49.1
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+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"),
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Bugfix to correctly deal with a GeneSetCollection object as input gene sets, when the input expression data is a SingleCellExperiment object

Robert Castelo authored on 01/06/2023 09:38:07
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 Package: GSVA
2 
-Version: 1.49.0
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+Version: 1.49.1
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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"),
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              person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"),
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bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:19:44
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 Package: GSVA
2 
-Version: 1.48.0
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+Version: 1.49.0
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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"),
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              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_17 branch

J Wokaty authored on 25/04/2023 14:19:44
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1 1 
 Package: GSVA
2 
-Version: 1.47.3
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+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"),
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              person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"),
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Merge pull request #82 from rcastelo/devel

merge in changes to devel

Axel Klenk authored on 17/04/2023 13:56:58 • GitHub committed on 17/04/2023 13:56:58
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Updated URL in inst/CITATION file to fix an --as-cran NOTE

Robert Castelo authored on 17/04/2023 08:20:49
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1 1 
 Package: GSVA
2 
-Version: 1.47.2
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+Version: 1.47.3
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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"),
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              person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"),
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Bump version

Robert Castelo authored on 17/04/2023 08:18:41
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1 1 
 Package: GSVA
2 
-Version: 1.47.1
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+Version: 1.47.2
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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"),
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              person("Justin", "Guinney", role="aut", email="jguinney@gmail.com"),
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Bump version

Robert Castelo authored on 17/04/2023 08:05:51
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1 1 
 Package: GSVA
2 
-Version: 1.47.0
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+Version: 1.47.1
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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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fix issue #73: add zscore method parameter class and constructor (and a virtual superclass)

Axel Klenk authored on 03/04/2023 15:30:44
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@@ -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
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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
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-Version: 1.46.0
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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"),
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              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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 Package: GSVA
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-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
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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"),
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Updated NEWS file

Robert Castelo authored on 31/10/2022 15:48:30
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 Package: GSVA
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-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
4 4 
 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"),
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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
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-Version: 1.45.4
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+Version: 1.45.5
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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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+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"),
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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"))
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
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-Version: 1.45.3
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+Version: 1.45.4
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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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@@ -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"))
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 Depends: R (>= 3.5.0)
9 9 
 Imports: methods, stats, utils, graphics, S4Vectors, IRanges,
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-         Biobase, SummarizedExperiment, GSEABase, Matrix, parallel,
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+         Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel,
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          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
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-Version: 1.45.2
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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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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
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-Version: 1.45.1
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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"),
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              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
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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 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
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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_15 branch

Nitesh Turaga authored on 26/04/2022 15:07:47
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 Package: GSVA
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-Version: 1.43.1
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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"),
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              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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 Package: GSVA
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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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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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 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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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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 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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Fixed unit test and updated NEWS file

[rcastelo] authored on 25/10/2021 15:10:55
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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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1 1 
 Package: GSVA
2 
-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
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 CITATION.cff file

Robert Castelo authored on 28/07/2021 12:03:18
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1 1 
 Package: GSVA
2 
-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
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

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
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"),
Browse code

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
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"),
Browse code

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
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"),
Browse code

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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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"),
Browse code

take out shinythemes from global

pablo-rodr-bio2 authored on 18/05/2021 10:28:35
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@@ -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"),
Browse code

new css changes in dashboard

pablo-rodr-bio2 authored on 17/05/2021 17:29:04
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@@ -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"),
Browse code

beautifying UI

pablo-rodr-bio2 authored on 14/05/2021 09:37:52
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History View file @ 7c64d7b
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@@ -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"),
Browse code

added css for title and btns

pablo-rodr-bio2 authored on 13/05/2021 11:26:15
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DESCRIPTION
History View file @ 002d7c7
... ... 
@@ -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)
Browse code

changed version

pablo-rodr-bio2 authored on 11/05/2021 15:31:56
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History View file @ b56bfec
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@@ -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"),
Browse code

removed filterFeatureSparse()

pablo-rodr-bio2 authored on 03/05/2021 12:24:35
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@@ -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"),
Browse code

added minor css to title

pablo-rodr-bio2 authored on 30/04/2021 10:26:32
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History View file @ 74f0a07
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@@ -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"),
Browse code

method in x label, args change with method

pablo-rodr-bio2 authored on 29/04/2021 17:41:04
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@@ -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"),
Browse code

modularizing and fixing bugs

pablo-rodr-bio2 authored on 26/04/2021 10:56:26
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History View file @ 96a8158
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@@ -1,9 +1,5 @@
1 1 
 Package: GSVA
2 
-<<<<<<< HEAD
3 
-Version: 1.39.24
4 
-=======
5 
-Version: 1.39.23
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->>>>>>> 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
Browse code

rebased

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

rebased

pablo-rodr-bio2 authored on 22/04/2021 16:03:37
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History View file @ 9a34d10
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@@ -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
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-          plotly, shinyjs, future, promises, shinybusy
30 
->>>>>>> modules in shinyApp
31 
-=======
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-          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
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DESCRIPTION
History View file @ 055f280
... ... 
@@ -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
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DESCRIPTION
History View file @ e32501d
... ... 
@@ -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
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DESCRIPTION
History View file @ ca2b622
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@@ -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
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DESCRIPTION
History View file @ 8a63510
... ... 
@@ -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
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DESCRIPTION
History View file @ 6118471
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@@ -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 @ 464936e
... ... 
@@ -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 @ 98c1bac
... ... 
@@ -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
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DESCRIPTION
History View file @ f2b69b6
... ... 
@@ -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
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DESCRIPTION
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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
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DESCRIPTION
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@@ -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
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DESCRIPTION
History View file @ 49edead
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@@ -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
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DESCRIPTION
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@@ -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
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DESCRIPTION
History View file @ 98d91f5
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@@ -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
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DESCRIPTION
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@@ -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
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DESCRIPTION
History View file @ b77eaec
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@@ -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
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DESCRIPTION
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... ... 
@@ -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
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DESCRIPTION
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@@ -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
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DESCRIPTION
History View file @ 1a9a435
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@@ -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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DESCRIPTION
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@@ -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"),
Browse code

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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DESCRIPTION
History View file @ 8226937
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@@ -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"),
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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DESCRIPTION
History View file @ 1e5b296
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@@ -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
Browse code

added ssgsea method for DelayedArray

pablo-rodr-bio2 authored on 15/12/2020 13:14:39
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DESCRIPTION
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@@ -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"),
Browse code

added delayed support for zscore method

pablo-rodr-bio2 authored on 02/12/2020 17:31:38
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DESCRIPTION
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@@ -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"),
Browse code

Bumped version.

Robert Castelo authored on 26/11/2020 12:22:45
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@@ -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"),
Browse code

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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DESCRIPTION
History View file @ 9908379
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@@ -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"),
Browse code

added delayed support for plage method

pablo-rodr-bio2 authored on 24/11/2020 16:56:20
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DESCRIPTION
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@@ -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"),
Browse code

added hdf5 support for plage method

pablo-rodr-bio2 authored on 20/11/2020 18:38:41
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DESCRIPTION
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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"),
... ... 
@@ -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.
Browse code

adding sparse support to method ssgsea

pablo-rodr-bio2 authored on 13/11/2020 12:45:26
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DESCRIPTION
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@@ -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.
Browse code

adding sparse support to zscore method

pablo-rodr-bio2 authored on 11/11/2020 19:13:24
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 Package: GSVA
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-Version: 1.39.5
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+Version: 1.39.6
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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 sparse support to method plage

pablo-rodr-bio2 authored on 10/11/2020 11:04:28
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 Package: GSVA
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-Version: 1.39.4
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+Version: 1.39.5
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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 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
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