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

J Wokaty authored on 01/11/2022 15:07:52
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.38.0
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+Version: 1.39.0
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 Date: 2012-03-16
6 6 
 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@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 15:07:52
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.37.1
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+Version: 1.38.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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remove require(GOstats) and negative weights in call to function layout.fruchterman.reingold

Anne Biton authored on 07/09/2022 23:53:07
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.37.0
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+Version: 1.37.1
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 15:13:35
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.36.0
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+Version: 1.37.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 15:13:35
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.35.0
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+Version: 1.36.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 16:06:44
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.34.0
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+Version: 1.35.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 16:06:44
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.33.0
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+Version: 1.34.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:57:33
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.32.0
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+Version: 1.33.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:57:33
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.31.0
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+Version: 1.32.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 14:49:15
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.30.0
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+Version: 1.31.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:49:15
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.29.0
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+Version: 1.30.0
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 Date: 2012-03-16
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 Author: Anne Biton
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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 18:33:06
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.28.0
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+Version: 1.29.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 18:33:06
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.27.0
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+Version: 1.28.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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replace wrong use of parallal foreach in function clusterFastICARuns by future_lapply or lapply

Anne Biton authored on 09/04/2020 09:43:12
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@@ -22,7 +22,7 @@ Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
22 22 
 Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
23 23 
 Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
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         breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
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-        breastCancerVDX
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+        breastCancerVDX, future, future.apply
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 Enhances: doMC
27 27 
 Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
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         'methods-MineICAParams.R' 'compareAnalysis.R'
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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 17:36:34
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1 1 
 Package: MineICA
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 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.26.0
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+Version: 1.27.0
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 Date: 2012-03-16
6 6 
 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 17:08:37
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.25.0
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+Version: 1.26.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 16:11:20
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1 1 
 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.24.0
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+Version: 1.25.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 15:53:40
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.23.0
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+Version: 1.24.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 15:54:31
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.22.0
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+Version: 1.23.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 15:41:50
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.21.0
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+Version: 1.22.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 14:41:39
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.20.0
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+Version: 1.21.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 14:35:29
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.19.0
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+Version: 1.20.0
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 Date: 2012-03-16
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 16:52:41
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 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.18.0
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+Version: 1.19.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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 16:39:59
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.17.0
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 Date: 2012-03-16
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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/MineICA@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.16.0
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+Version: 1.17.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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/MineICA@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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1 1 
 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.15.0
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+Version: 1.16.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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/MineICA@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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1 1 
 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.14.0
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+Version: 1.15.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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/MineICA@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.13.0
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+Version: 1.14.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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bump version after creating 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:30:44
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.12.0
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+Version: 1.13.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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Bump versions prior to creation of 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:20:18
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.11.0
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+Version: 1.12.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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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/MineICA@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.10.0
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+Version: 1.11.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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Bumped versions of all packages prior to creating 3.2 branch.

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

Dan Tenenbaum authored on 13/10/2015 19:36:05
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.9.0
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+Version: 1.10.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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Bump versions in trunk after creation of 3.1 branch.

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

Dan Tenenbaum authored on 16/04/2015 20:02:44
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.8.0
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+Version: 1.9.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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Bump versions prior to creating 3.1 branch.

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

Dan Tenenbaum authored on 16/04/2015 19:42:01
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 Package: MineICA
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.7.1
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+Version: 1.8.0
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

Remove locally defined "organism" and "organism<-" generics (the former was actually defined twice) and import BiocGenerics so the locally defined methods get attached to the new "organism" and "organism<-" generics from BiocGenerics. Also remove the "getOrganism" and "setOrganism" generics and methods. They were (a) not exported (even though the class-IcaSet.Rd man pages contained aliases for them), (b) not used internally, and (c) redundant with the "organism" and "organism<-" methods.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@100850 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 19/03/2015 00:33:15
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1 1 
 Package: MineICA
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 Type: Package
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 Title: Analysis of an ICA decomposition obtained on genomics data
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-Version: 1.7.0
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+Version: 1.7.1
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 Date: 2012-03-16
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 Author: Anne Biton
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 Maintainer: Anne Biton <anne.biton@gmail.com>
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@@ -15,11 +15,11 @@ Description: The goal of MineICA is to perform Independent Component
15 15 
         graph.
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 License: GPL-2
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 LazyLoad: yes
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+Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
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+        ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster,
20 
+        marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph,
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+        annotate, Hmisc, fastICA, JADE
18 22 
 Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
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-Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable,
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-        biomaRt, gtools, GOstats, cluster, marray, mclust,
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-        RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate,
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-        Hmisc, fastICA, JADE, methods
23 23 
 Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
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         breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
25 25 
         breastCancerVDX
Browse code

Bumping versions after creating 3.0 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@95443 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:47:41
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.6.0
4 
+Version: 1.7.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

Bump package versions prior to creating the 3.0 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@95439 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:38:33
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.5.1
4 
+Version: 1.6.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

biocViews update

- update redundant biocViews


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@91223 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 10/06/2014 23:34:33
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.5.0
4 
+Version: 1.5.1
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
... ... 
@@ -29,4 +29,4 @@ Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
29 29 
         'functions_comp2annot.R' 'functions_comp2annottests.R'
30 30 
         'functions_enrich.R' 'functions.R' 'heatmap.plus.R'
31 31 
         'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'
32 
-biocViews: Visualizations, MultipleComparison
32 
+biocViews: Visualization, MultipleComparison
Browse code

Second version bump after creating 2.14 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@88840 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:21:21
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.4.0
4 
+Version: 1.5.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

First version bump prior to creating 2.14 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@88838 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:07:21
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DESCRIPTION
History View file @ 16907cc
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.3.3
4 
+Version: 1.4.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

modify to new biocViews to DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@87035 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 04/03/2014 22:12:21
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DESCRIPTION
History View file @ 45bf2e0
... ... 
@@ -1,72 +1,32 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.3.2
4 
+Version: 1.3.3
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
8 
-Description: The goal of MineICA is to perform Independent Component Analysis
9 
-    (ICA) on multiple transcriptome datasets, integrating additional data (e.g
10 
-    molecular, clinical and pathological). This Integrative ICA helps the
11 
-    biological interpretation of the components by studying their association
12 
-    with variables (e.g sample annotations) and gene sets, and enables the
13 
-    comparison of components from different datasets using correlation-based
14 
-    graph.
8 
+Description: The goal of MineICA is to perform Independent Component
9 
+        Analysis (ICA) on multiple transcriptome datasets, integrating
10 
+        additional data (e.g molecular, clinical and pathological).
11 
+        This Integrative ICA helps the biological interpretation of the
12 
+        components by studying their association with variables (e.g
13 
+        sample annotations) and gene sets, and enables the comparison
14 
+        of components from different datasets using correlation-based
15 
+        graph.
15 16 
 License: GPL-2
16 17 
 LazyLoad: yes
17 
-BiocViews: Bioinformatics, Visualizations, MultipleComparisons
18 
-Imports:
19 
-    AnnotationDbi,
20 
-    lumi,
21 
-    fpc,
22 
-    lumiHumanAll.db
23 
-Depends:
24 
-    R (>= 2.10),
25 
-    Biobase,
26 
-    plyr,
27 
-    ggplot2,
28 
-    scales,
29 
-    foreach,
30 
-    xtable,
31 
-    biomaRt,
32 
-    gtools,
33 
-    GOstats,
34 
-    cluster,
35 
-    marray,
36 
-    mclust,
37 
-    RColorBrewer,
38 
-    colorspace,
39 
-    igraph,
40 
-    Rgraphviz,
41 
-    graph,
42 
-    annotate,
43 
-    Hmisc,
44 
-    fastICA,
45 
-    JADE,
46 
-    methods
47 
-Suggests:
48 
-    biomaRt,
49 
-    GOstats,
50 
-    cluster,
51 
-    hgu133a.db,
52 
-    mclust,
53 
-    igraph,
54 
-    breastCancerMAINZ,
55 
-    breastCancerTRANSBIG,
56 
-    breastCancerUPP,
57 
-    breastCancerVDX
18 
+Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
19 
+Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable,
20 
+        biomaRt, gtools, GOstats, cluster, marray, mclust,
21 
+        RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate,
22 
+        Hmisc, fastICA, JADE, methods
23 
+Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
24 
+        breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
25 
+        breastCancerVDX
58 26 
 Enhances: doMC
59 
-Collate:
60 
-    'AllClasses.R'
61 
-    'AllGeneric.R'
62 
-    'methods-IcaSet.R'
63 
-    'methods-MineICAParams.R'
64 
-    'compareAnalysis.R'
65 
-    'functions_comp2annot.R'
66 
-    'functions_comp2annottests.R'
67 
-    'functions_enrich.R'
68 
-    'functions.R'
69 
-    'heatmap.plus.R'
70 
-    'heatmapsOnSel.R'
71 
-    'runAn.R'
72 
-    'compareGenes.R'
27 
+Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
28 
+        'methods-MineICAParams.R' 'compareAnalysis.R'
29 
+        'functions_comp2annot.R' 'functions_comp2annottests.R'
30 
+        'functions_enrich.R' 'functions.R' 'heatmap.plus.R'
31 
+        'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'
32 
+biocViews: Visualizations, MultipleComparison
Browse code

Correction of the vignette. Made sure breaks are taken into accounts in heatmap.plus function.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@83955 bc3139a8-67e5-0310-9ffc-ced21a209358

Anne Biton authored on 05/12/2013 20:29:39
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.3.1
4 
+Version: 1.3.2
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

Bump version number after correction of the vignette.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@83835 bc3139a8-67e5-0310-9ffc-ced21a209358

Anne Biton authored on 03/12/2013 02:47:21
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DESCRIPTION
History View file @ f134765
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.3.0
4 
+Version: 1.3.1
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

bump version after release branch has been created

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@81644 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:47:19
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.2.0
4 
+Version: 1.3.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

bump versions prior to creating BioC 2.13 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@81642 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:29:21
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DESCRIPTION
History View file @ dfbe248
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.1.0
4 
+Version: 1.2.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

geom_jitter was used to superimpose points on boxplots (when 'addPoints = TRUE' in function qualVarAnalysis)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@79893 bc3139a8-67e5-0310-9ffc-ced21a209358

Anne Biton authored on 28/08/2013 18:26:23
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DESCRIPTION
History View file @ b10fe98
... ... 
@@ -5,12 +5,13 @@ Version: 1.1.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
8 
-Description: The goal of MineICA is to make easier the interpretation of the
9 
-    interpretation of a decomposition obtained by Independent Component
10 
-    Analysis on transcriptomic data. It helps the biological interpretation of
11 
-    the components by studying their association with variables (e.g sample
12 
-    annotations) and gene sets, and enables the comparison of components from
13 
-    different datasets using correlation-based graph.
8 
+Description: The goal of MineICA is to perform Independent Component Analysis
9 
+    (ICA) on multiple transcriptome datasets, integrating additional data (e.g
10 
+    molecular, clinical and pathological). This Integrative ICA helps the
11 
+    biological interpretation of the components by studying their association
12 
+    with variables (e.g sample annotations) and gene sets, and enables the
13 
+    comparison of components from different datasets using correlation-based
14 
+    graph.
14 15 
 License: GPL-2
15 16 
 LazyLoad: yes
16 17 
 BiocViews: Bioinformatics, Visualizations, MultipleComparisons
Browse code

Bump y in version x.y.z to odd number in devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@75270 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 22:06:11
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DESCRIPTION
History View file @ a9670cd
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 1.0.0
4 
+Version: 1.1.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

bump y of x.y.z version number for BioC 2.12 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@75263 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 21:32:27
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History View file @ 6b2e88d
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@@ -1,7 +1,7 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 0.99.1
4 
+Version: 1.0.0
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: Anne Biton <anne.biton@gmail.com>
Browse code

add maintainer name to Maintainer field

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@74514 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 18/03/2013 17:58:38
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DESCRIPTION
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... ... 
@@ -4,7 +4,7 @@ Title: Analysis of an ICA decomposition obtained on genomics data
4 4 
 Version: 0.99.1
5 5 
 Date: 2012-03-16
6 6 
 Author: Anne Biton
7 
-Maintainer: <anne.biton@gmail.com>
7 
+Maintainer: Anne Biton <anne.biton@gmail.com>
8 8 
 Description: The goal of MineICA is to make easier the interpretation of the
9 9 
     interpretation of a decomposition obtained by Independent Component
10 10 
     Analysis on transcriptomic data. It helps the biological interpretation of
Browse code

Update version numbering from 0.1.0 to 0.99.1, remove three help files of data not available in the package anymore.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@74468 bc3139a8-67e5-0310-9ffc-ced21a209358

Anne Biton authored on 16/03/2013 19:22:39
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DESCRIPTION
History View file @ 5559282
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: MineICA
2 2 
 Type: Package
3 3 
 Title: Analysis of an ICA decomposition obtained on genomics data
4 
-Version: 0.1.0
5 
-Date: 2012-01-21
4 
+Version: 0.99.1
5 
+Date: 2012-03-16
6 6 
 Author: Anne Biton
7 7 
 Maintainer: <anne.biton@gmail.com>
8 8 
 Description: The goal of MineICA is to make easier the interpretation of the
... ... 
@@ -14,17 +14,58 @@ Description: The goal of MineICA is to make easier the interpretation of the
14 14 
 License: GPL-2
15 15 
 LazyLoad: yes
16 16 
 BiocViews: Bioinformatics, Visualizations, MultipleComparisons
17 
-Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
18 
-Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable,
19 
-        biomaRt, gtools, GOstats, cluster, marray, mclust,
20 
-        RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate,
21 
-        Hmisc, fastICA, JADE, methods
22 
-Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
23 
-        breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
24 
-        breastCancerVDX
17 
+Imports:
18 
+    AnnotationDbi,
19 
+    lumi,
20 
+    fpc,
21 
+    lumiHumanAll.db
22 
+Depends:
23 
+    R (>= 2.10),
24 
+    Biobase,
25 
+    plyr,
26 
+    ggplot2,
27 
+    scales,
28 
+    foreach,
29 
+    xtable,
30 
+    biomaRt,
31 
+    gtools,
32 
+    GOstats,
33 
+    cluster,
34 
+    marray,
35 
+    mclust,
36 
+    RColorBrewer,
37 
+    colorspace,
38 
+    igraph,
39 
+    Rgraphviz,
40 
+    graph,
41 
+    annotate,
42 
+    Hmisc,
43 
+    fastICA,
44 
+    JADE,
45 
+    methods
46 
+Suggests:
47 
+    biomaRt,
48 
+    GOstats,
49 
+    cluster,
50 
+    hgu133a.db,
51 
+    mclust,
52 
+    igraph,
53 
+    breastCancerMAINZ,
54 
+    breastCancerTRANSBIG,
55 
+    breastCancerUPP,
56 
+    breastCancerVDX
25 57 
 Enhances: doMC
26 
-Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
27 
-        'methods-MineICAParams.R' 'compareAnalysis.R'
28 
-        'functions_comp2annot.R' 'functions_comp2annottests.R'
29 
-        'functions_enrich.R' 'functions.R' 'heatmap.plus.R'
30 
-        'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'
58 
+Collate:
59 
+    'AllClasses.R'
60 
+    'AllGeneric.R'
61 
+    'methods-IcaSet.R'
62 
+    'methods-MineICAParams.R'
63 
+    'compareAnalysis.R'
64 
+    'functions_comp2annot.R'
65 
+    'functions_comp2annottests.R'
66 
+    'functions_enrich.R'
67 
+    'functions.R'
68 
+    'heatmap.plus.R'
69 
+    'heatmapsOnSel.R'
70 
+    'runAn.R'
71 
+    'compareGenes.R'
Browse code

Adds MineICA, SomatiCA and lpNet to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 05/02/2013 22:15:53
Showing 1 changed files
DESCRIPTION
History View file @ 14753e6
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,30 @@
1 
+Package: MineICA
2 
+Type: Package
3 
+Title: Analysis of an ICA decomposition obtained on genomics data
4 
+Version: 0.1.0
5 
+Date: 2012-01-21
6 
+Author: Anne Biton
7 
+Maintainer: <anne.biton@gmail.com>
8 
+Description: The goal of MineICA is to make easier the interpretation of the
9 
+    interpretation of a decomposition obtained by Independent Component
10 
+    Analysis on transcriptomic data. It helps the biological interpretation of
11 
+    the components by studying their association with variables (e.g sample
12 
+    annotations) and gene sets, and enables the comparison of components from
13 
+    different datasets using correlation-based graph.
14 
+License: GPL-2
15 
+LazyLoad: yes
16 
+BiocViews: Bioinformatics, Visualizations, MultipleComparisons
17 
+Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
18 
+Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable,
19 
+        biomaRt, gtools, GOstats, cluster, marray, mclust,
20 
+        RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate,
21 
+        Hmisc, fastICA, JADE, methods
22 
+Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
23 
+        breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
24 
+        breastCancerVDX
25 
+Enhances: doMC
26 
+Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
27 
+        'methods-MineICAParams.R' 'compareAnalysis.R'
28 
+        'functions_comp2annot.R' 'functions_comp2annottests.R'
29 
+        'functions_enrich.R' 'functions.R' 'heatmap.plus.R'
30 
+        'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'