1. edge
  2. DESCRIPTION
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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 14:39:41
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 Type: Package
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 Title: Extraction of Differential Gene Expression
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 Date: 2015-04-15
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-Version: 2.32.0
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+Version: 2.33.0
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 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@emory.edu>
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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 14:39:41
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 Type: Package
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 Title: Extraction of Differential Gene Expression
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-Version: 2.31.0
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+Version: 2.32.0
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 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@emory.edu>
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updated email

Andrew Bass authored on 20/11/2022 20:30:22
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 Version: 2.31.0
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 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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-    <ajbass@princeton.edu>
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+    <ajbass@emory.edu>
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 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
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     Regression, GeneExpression, DataImport
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 Description: The edge package implements methods for carrying out differential
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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 15:11:40
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 Title: Extraction of Differential Gene Expression
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-Version: 2.30.0
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+Version: 2.31.0
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 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.edu>
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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 15:11:40
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 Title: Extraction of Differential Gene Expression
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-Version: 2.29.1
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+Version: 2.30.0
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.edu>
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remove jackstraw dependence

Andrew Bass authored on 10/09/2022 22:18:17
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-Version: 2.29.0
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     <ajbass@princeton.edu>
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@@ -22,7 +22,6 @@ Imports:
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     splines,
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     sva,
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     snm,
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-    jackstraw,
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     qvalue(>= 1.99.0),
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     MASS
28 27 
 Suggests:
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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 15:25:27
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-Version: 2.28.0
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.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 15:25:27
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 Title: Extraction of Differential Gene Expression
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-Version: 2.27.0
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.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 16:20:40
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 Title: Extraction of Differential Gene Expression
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-Version: 2.26.0
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.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 16:20:40
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     <ajbass@princeton.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 16:13:39
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 Title: Extraction of Differential Gene Expression
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-Version: 2.24.0
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.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 16:13:39
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-Version: 2.23.0
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.edu>
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bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:05:22
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-Version: 2.22.0
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     <ajbass@princeton.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 15:05:22
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-Version: 2.21.0
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     <ajbass@princeton.edu>
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bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:49:03
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     <ajbass@princeton.edu>
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:49:03
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-Version: 2.19.0
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     <ajbass@princeton.edu>
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bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:39:25
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-Version: 2.18.0
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     <ajbass@princeton.edu>
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bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:09:18
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     <ajbass@princeton.edu>
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bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:12:42
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-Version: 2.16.0
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     <ajbass@princeton.edu>
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bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:55
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 Title: Extraction of Differential Gene Expression
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     <ajbass@princeton.edu>
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bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:34
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     <ajbass@princeton.edu>
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bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:58
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     <ajbass@princeton.edu>
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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:48:05
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-Version: 2.13.1
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 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
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     <ajbass@princeton.edu>
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bump

Andrew Bass authored on 30/08/2018 12:39:55
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     <ajbass@princeton.edu>
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bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:41
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     <ajbass@princeton.edu>
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bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:37
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     <ajbass@princeton.edu>
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bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:54:10
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-Version: 2.10.0
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     <ajbass@princeton.edu>
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bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:40:51
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     <ajbass@princeton.edu>
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bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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     <ajbass@princeton.edu>
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bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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     <ajbass@princeton.edu>
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bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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     <ajbass@princeton.edu>
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create a valid ExpressionSet()

- exprs(obj) <- value does not sync dimnames(value) with dimnames(obj)


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@120628 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 31/08/2016 22:08:32
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     <ajbass@princeton.edu>
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Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 15/05/2016 20:14:22
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Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/05/2016 23:05:31
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@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.5.0
5 
+Version: 2.5.1
6 6 
 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 7 
 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
8 8 
     <ajbass@princeton.edu>
Browse code

bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.4.0
5 
+Version: 2.5.0
6 6 
 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 7 
 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
8 8 
     <ajbass@princeton.edu>
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
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@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.3.1
5 
+Version: 2.4.0
6 6 
 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 7 
 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
8 8 
     <ajbass@princeton.edu>
Browse code

fixed error message (jackstraw was updated)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@112239 bc3139a8-67e5-0310-9ffc-ced21a209358

Andrew Bass authored on 06/01/2016 18:41:38
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... ... 
@@ -2,19 +2,20 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.3.0
5 
+Version: 2.3.1
6 6 
 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 
-Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
7 
+Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass
8 
+    <ajbass@princeton.edu>
8 9 
 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
9 10 
     Regression, GeneExpression, DataImport
10 11 
 Description: The edge package implements methods for carrying out differential
11 
-    expression analyses of genome-wide gene expression studies. Significance
12 
-    testing using the optimal discovery procedure and generalized likelihood
13 
-    ratio tests (equivalent to F-tests and t-tests) are implemented for general study
14 
-    designs. Special functions are available to facilitate the analysis of
15 
-    common study designs, including time course experiments. Other packages
16 
-    such as snm, sva, and qvalue are integrated in edge to provide a wide range
17 
-    of tools for gene expression analysis.
12 
+    expression analyses of genome-wide gene expression studies. Significance testing
13 
+    using the optimal discovery procedure and generalized likelihood ratio tests
14 
+    (equivalent to F-tests and t-tests) are implemented for general study designs.
15 
+    Special functions are available to facilitate the analysis of common study
16 
+    designs, including time course experiments. Other packages such as snm, sva,
17 
+    and qvalue are integrated in edge to provide a wide range of tools for gene
18 
+    expression analysis.
18 19 
 VignetteBuilder: knitr
19 20 
 Imports:
20 21 
     methods,
... ... 
@@ -37,3 +38,4 @@ BugReports: https://github.com/jdstorey/edge/issues
37 38 
 LazyData: true
38 39 
 License: MIT + file LICENSE
39 40 
 NeedsCompilation: yes
41 
+RoxygenNote: 5.0.1
Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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History View file @ 782a124
... ... 
@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.2.0
5 
+Version: 2.3.0
6 6 
 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 7 
 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
8 8 
 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.1.1
5 
+Version: 2.2.0
6 6 
 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 7 
 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
8 8 
 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
Browse code

Update to edge 2.1.1.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@109554 bc3139a8-67e5-0310-9ffc-ced21a209358

John D Storey authored on 13/10/2015 01:16:14
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History View file @ cbcd0be
... ... 
@@ -2,13 +2,9 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.1.0
6 
-Authors@R: c(
7 
-    person("John D.", "Storey", email = "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 
-    person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role = c("aut")),
9 
-    person("Andrew J.", "Bass", email = "ajbass@princeton.edu", role = c("aut"))
10 
-    )
11 
-Maintainer: John D. Storey <jstorey@princeton.edu>
5 
+Version: 2.1.1
6 
+Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass
7 
+Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@princeton.edu>
12 8 
 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
13 9 
     Regression, GeneExpression, DataImport
14 10 
 Description: The edge package implements methods for carrying out differential
... ... 
@@ -25,6 +21,7 @@ Imports:
25 21 
     splines,
26 22 
     sva,
27 23 
     snm,
24 
+    jackstraw,
28 25 
     qvalue(>= 1.99.0),
29 26 
     MASS
30 27 
 Suggests:
... ... 
@@ -33,7 +30,7 @@ Suggests:
33 30 
     ggplot2,
34 31 
     reshape2
35 32 
 Depends:
36 
-    R(>= 3.2.0),
33 
+    R(>= 3.1.0),
37 34 
     Biobase
38 35 
 URL: https://github.com/jdstorey/edge
39 36 
 BugReports: https://github.com/jdstorey/edge/issues
Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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History View file @ 50c9ca0
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@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 2.0.0
5 
+Version: 2.1.0
6 6 
 Authors@R: c(
7 7 
     person("John D.", "Storey", email = "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 8 
     person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role = c("aut")),
Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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@@ -2,7 +2,7 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-04-15
5 
-Version: 1.99.1
5 
+Version: 2.0.0
6 6 
 Authors@R: c(
7 7 
     person("John D.", "Storey", email = "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 8 
     person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role = c("aut")),
Browse code

Improvements to the documentation.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@102555 bc3139a8-67e5-0310-9ffc-ced21a209358

John D Storey authored on 16/04/2015 03:12:02
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... ... 
@@ -1,31 +1,42 @@
1 1 
 Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 
-Date: 2015-03-26
5 
-Version: 1.99.0
6 
-Authors@R: c( person("John D.", "Storey", email =
7 
-        "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 
-        person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role =
9 
-        c("aut")), person("Andrew J.", "Bass", email =
10 
-        "ajbass@princeton.edu", role = c("aut")) )
4 
+Date: 2015-04-15
5 
+Version: 1.99.1
6 
+Authors@R: c(
7 
+    person("John D.", "Storey", email = "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 
+    person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role = c("aut")),
9 
+    person("Andrew J.", "Bass", email = "ajbass@princeton.edu", role = c("aut"))
10 
+    )
11 
+Maintainer: John D. Storey <jstorey@princeton.edu>
11 12 
 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
12 
-        Regression, GeneExpression, DataImport
13 
-Description: The edge package implements methods for carrying out
14 
-        differential expression analyses of genome-wide gene expression
15 
-        studies. Significance testing using the optimal discovery
16 
-        procedure and generalized likelihood ratio tests (equivalent to
17 
-        F-tests and t-tests) are implemented for general study designs.
18 
-        Special functions are available to facilitate the analysis of
19 
-        common study designs, including time course experiments. Other
20 
-        packages such as snm, sva, and qvalue are integrated in edge to
21 
-        provide a wide range of tools for gene expression analysis.
13 
+    Regression, GeneExpression, DataImport
14 
+Description: The edge package implements methods for carrying out differential
15 
+    expression analyses of genome-wide gene expression studies. Significance
16 
+    testing using the optimal discovery procedure and generalized likelihood
17 
+    ratio tests (equivalent to F-tests and t-tests) are implemented for general study
18 
+    designs. Special functions are available to facilitate the analysis of
19 
+    common study designs, including time course experiments. Other packages
20 
+    such as snm, sva, and qvalue are integrated in edge to provide a wide range
21 
+    of tools for gene expression analysis.
22 22 
 VignetteBuilder: knitr
23 
-Imports: methods, splines, sva, snm, qvalue(>= 1.99.0), MASS
24 
-Suggests: testthat, knitr, ggplot2, reshape2
25 
-Depends: R(>= 3.2.0), Biobase
23 
+Imports:
24 
+    methods,
25 
+    splines,
26 
+    sva,
27 
+    snm,
28 
+    qvalue(>= 1.99.0),
29 
+    MASS
30 
+Suggests:
31 
+    testthat,
32 
+    knitr,
33 
+    ggplot2,
34 
+    reshape2
35 
+Depends:
36 
+    R(>= 3.2.0),
37 
+    Biobase
26 38 
 URL: https://github.com/jdstorey/edge
27 39 
 BugReports: https://github.com/jdstorey/edge/issues
28 40 
 LazyData: true
29 
-License: GPL
30 
-Copyright: 2005-2015 John D. Storey
41 
+License: MIT + file LICENSE
31 42 
 NeedsCompilation: yes
Browse code

- update version to 1.99.0 so that edge releases as 2.0.0 - remove maintainer and author field as Authors@R is already present

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@102536 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 15/04/2015 20:02:45
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@@ -2,13 +2,12 @@ Package: edge
2 2 
 Type: Package
3 3 
 Title: Extraction of Differential Gene Expression
4 4 
 Date: 2015-03-26
5 
-Version: 0.99.4
5 
+Version: 1.99.0
6 6 
 Authors@R: c( person("John D.", "Storey", email =
7 7 
         "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 8 
         person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role =
9 9 
         c("aut")), person("Andrew J.", "Bass", email =
10 10 
         "ajbass@princeton.edu", role = c("aut")) )
11 
-Maintainer: John D. Storey <jstorey@princeton.edu>
12 11 
 biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
13 12 
         Regression, GeneExpression, DataImport
14 13 
 Description: The edge package implements methods for carrying out
... ... 
@@ -30,5 +29,3 @@ LazyData: true
30 29 
 License: GPL
31 30 
 Copyright: 2005-2015 John D. Storey
32 31 
 NeedsCompilation: yes
33 
-Author: John D. Storey [aut, cre, cph], Jeffrey T. Leek [aut], Andrew
34 
-        J. Bass [aut]
Browse code

add packages to the repository

edge/ pwOmics/ EMDomics/



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edge@102444 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 14/04/2015 17:06:48
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1 1 
new file mode 100644
... ... 
@@ -0,0 +1,34 @@
1 
+Package: edge
2 
+Type: Package
3 
+Title: Extraction of Differential Gene Expression
4 
+Date: 2015-03-26
5 
+Version: 0.99.4
6 
+Authors@R: c( person("John D.", "Storey", email =
7 
+        "jstorey@princeton.edu", role = c("aut", "cre", "cph")),
8 
+        person("Jeffrey T.", "Leek", email = "jleek@jhsph.edu ", role =
9 
+        c("aut")), person("Andrew J.", "Bass", email =
10 
+        "ajbass@princeton.edu", role = c("aut")) )
11 
+Maintainer: John D. Storey <jstorey@princeton.edu>
12 
+biocViews: MultipleComparison, DifferentialExpression, TimeCourse,
13 
+        Regression, GeneExpression, DataImport
14 
+Description: The edge package implements methods for carrying out
15 
+        differential expression analyses of genome-wide gene expression
16 
+        studies. Significance testing using the optimal discovery
17 
+        procedure and generalized likelihood ratio tests (equivalent to
18 
+        F-tests and t-tests) are implemented for general study designs.
19 
+        Special functions are available to facilitate the analysis of
20 
+        common study designs, including time course experiments. Other
21 
+        packages such as snm, sva, and qvalue are integrated in edge to
22 
+        provide a wide range of tools for gene expression analysis.
23 
+VignetteBuilder: knitr
24 
+Imports: methods, splines, sva, snm, qvalue(>= 1.99.0), MASS
25 
+Suggests: testthat, knitr, ggplot2, reshape2
26 
+Depends: R(>= 3.2.0), Biobase
27 
+URL: https://github.com/jdstorey/edge
28 
+BugReports: https://github.com/jdstorey/edge/issues
29 
+LazyData: true
30 
+License: GPL
31 
+Copyright: 2005-2015 John D. Storey
32 
+NeedsCompilation: yes
33 
+Author: John D. Storey [aut, cre, cph], Jeffrey T. Leek [aut], Andrew
34 
+        J. Bass [aut]