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Revision: 97036
Author: a.akalin
Date: 2014-11-22T22:38:36+00:00
Paths:
Added  /trunk/madman/Rpacks/genomation/.Rbuildignore
Modified  /trunk/madman/Rpacks/genomation/.Rinstignore
Added  /trunk/madman/Rpacks/genomation/.gitignore
Modified  /trunk/madman/Rpacks/genomation/DESCRIPTION
Modified  /trunk/madman/Rpacks/genomation/NAMESPACE
Modified  /trunk/madman/Rpacks/genomation/NEWS
Modified  /trunk/madman/Rpacks/genomation/R/documentData.R
Modified  /trunk/madman/Rpacks/genomation/R/findFeatureComb.R
Modified  /trunk/madman/Rpacks/genomation/R/genomation-classes.R
Modified  /trunk/madman/Rpacks/genomation/R/getRandomEnrichment.R
Modified  /trunk/madman/Rpacks/genomation/R/plotMatrix.R
Modified  /trunk/madman/Rpacks/genomation/R/randomizeFeature.R
Modified  /trunk/madman/Rpacks/genomation/R/readAnnotate.R
Modified  /trunk/madman/Rpacks/genomation/R/readData.R
Modified  /trunk/madman/Rpacks/genomation/R/scoreMatrix.R
Modified  /trunk/madman/Rpacks/genomation/R/scoreMatrixBin.R
Modified  /trunk/madman/Rpacks/genomation/R/scoreMatrixList.R
Modified  /trunk/madman/Rpacks/genomation/README.md
Added  /trunk/madman/Rpacks/genomation/genomation.Rproj
Added  /trunk/madman/Rpacks/genomation/inst/doc
Added  /trunk/madman/Rpacks/genomation/inst/doc/Figures
Added  /trunk/madman/Rpacks/genomation/inst/doc/Figures/dataAnalysis.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/Figures/genomationFlowChart1.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresctcfScoreMatrixList.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresheatMatrix1.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresheatMatrix11.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresheatMatrix12.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresheatMatrix2.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresheatMatrixScales.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresmultiHeatMatrix1.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresmultiHeatMatrix2.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresplotGeneAnnotation1.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresplotGeneAnnotation2.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresplotScaledProfile.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/FiguresvisualizeFeatureComb.pdf
Added  /trunk/madman/Rpacks/genomation/inst/doc/GenomationManual-knitr.Rnw
Added  /trunk/madman/Rpacks/genomation/inst/doc/GenomationManual-knitr.pdf
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/EnhancersEncode.txt.Test
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/Fantom4.Cage.Test
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/chr21.CpGi.hg19.bed
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/chr21.refseq.hg19.bed
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/chr21.refseq.hg19.gtf
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/ex.broadPeak
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/ex.narrowPeak
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/tab1.bed
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/tab2.bed
Modified  /trunk/madman/Rpacks/genomation/inst/extdata/tab3.bed
Modified  /trunk/madman/Rpacks/genomation/inst/scripts/devtools_test.R
Modified  /trunk/madman/Rpacks/genomation/inst/scripts/produceDataForExamples.R
Modified  /trunk/madman/Rpacks/genomation/inst/tests/ScoreMatrixBinTests.R
Modified  /trunk/madman/Rpacks/genomation/inst/tests/ScoreMatrixListTests.R
Modified  /trunk/madman/Rpacks/genomation/inst/tests/ScoreMatrixTests.R
Modified  /trunk/madman/Rpacks/genomation/inst/tests/readDataTests.R
Modified  /trunk/madman/Rpacks/genomation/inst/tests/tab.test1
Modified  /trunk/madman/Rpacks/genomation/inst/tests/tab.test2
Modified  /trunk/madman/Rpacks/genomation/inst/tests/tab.test3
Modified  /trunk/madman/Rpacks/genomation/inst/tests/test.bedGraph
Modified  /trunk/madman/Rpacks/genomation/man/AnnotationByFeature-class.Rd
Modified  /trunk/madman/Rpacks/genomation/man/AnnotationByGeneParts-class.Rd
Modified  /trunk/madman/Rpacks/genomation/man/AnnotationByGeneParts-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/RandomEnrichment-class.Rd
Modified  /trunk/madman/Rpacks/genomation/man/ScoreMatrix-class.Rd
Modified  /trunk/madman/Rpacks/genomation/man/ScoreMatrix-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/ScoreMatrixBin-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/ScoreMatrixList-class.Rd
Modified  /trunk/madman/Rpacks/genomation/man/ScoreMatrixList-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/annotateWithFeature-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/annotateWithFeatureFlank-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/annotateWithGeneParts-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/binMatrix-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/cage.Rd
Modified  /trunk/madman/Rpacks/genomation/man/calculateOverlapSignificance-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/convertBed2Exons-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/convertBed2Introns-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/convertBedDf-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/cpgi.Rd
Modified  /trunk/madman/Rpacks/genomation/man/findFeatureComb-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/genes.Rd
Modified  /trunk/madman/Rpacks/genomation/man/getFeatsWithTargetsStats-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/getFlanks-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/getMembers-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/getRandomEnrichment-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/getTargetAnnotationStats-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/gffToGRanges.Rd
Modified  /trunk/madman/Rpacks/genomation/man/heatMatrix.Rd
Modified  /trunk/madman/Rpacks/genomation/man/heatMeta.Rd
Modified  /trunk/madman/Rpacks/genomation/man/intersectScoreMatrixList-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/multiHeatMatrix.Rd
Modified  /trunk/madman/Rpacks/genomation/man/orderBy-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/plotGeneAnnotation-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/plotMeta.Rd
Modified  /trunk/madman/Rpacks/genomation/man/plotTargetAnnotation-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/promoters.Rd
Modified  /trunk/madman/Rpacks/genomation/man/randomizeFeature-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/readBed.Rd
Modified  /trunk/madman/Rpacks/genomation/man/readBroadPeak.Rd
Modified  /trunk/madman/Rpacks/genomation/man/readFeatureFlank-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/readGeneric.Rd
Modified  /trunk/madman/Rpacks/genomation/man/readNarrowPeak.Rd
Modified  /trunk/madman/Rpacks/genomation/man/readTranscriptFeatures-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/scaleScoreMatrix-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/man/scaleScoreMatrixList.Rd
Modified  /trunk/madman/Rpacks/genomation/man/show-methods.Rd
Modified  /trunk/madman/Rpacks/genomation/vignettes/GenomationManual-knitr.Rnw
Added  /trunk/madman/Rpacks/genomation/vignettes/GenomationManual-knitr.pdf
Added  /trunk/madman/Rpacks/genomation/vignettes/cache
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixBinExample_d283d833c7660b5611f31dc8dc295ae9.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixBinExample_d283d833c7660b5611f31dc8dc295ae9.rdb
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Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixList_ed6fc83963faf636dc5a8b26ad2eb12e.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixList_ed6fc83963faf636dc5a8b26ad2eb12e.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixList_ed6fc83963faf636dc5a8b26ad2eb12e.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-__packages
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-annotateCtcf_5e207f303db628e51720928aa3a29ff4.RData
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Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-annotateTargetList_314918b004166ca9938d85285fd20e35.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-annotateTargetList_314918b004166ca9938d85285fd20e35.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-annotateTargetList_314918b004166ca9938d85285fd20e35.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-annotationHubExample1_f70ff1b165d0879e5fd118e4842ca263.RData
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Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ctcfScoreMatrixList_987b89ab33bbbd7e3083e0131d2ad441.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ctcfScoreMatrixList_987b89ab33bbbd7e3083e0131d2ad441.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ctcfScoreMatrixList_987b89ab33bbbd7e3083e0131d2ad441.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-findFeatureComb_5b7836c86ef51fabbf82f268986f4b65.RData
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Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readGff1_b3664bd5e56473034d853c8e5e52b508.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readGff1_b3664bd5e56473034d853c8e5e52b508.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readGff2_f74c8f72938b0a1796fd4c42a757a12b.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readGff2_f74c8f72938b0a1796fd4c42a757a12b.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readGff2_f74c8f72938b0a1796fd4c42a757a12b.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readTranscriptFeatures_97d12bc7984c4bed658fdcb630d6ebe5.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readTranscriptFeatures_97d12bc7984c4bed658fdcb630d6ebe5.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-readTranscriptFeatures_97d12bc7984c4bed658fdcb630d6ebe5.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-selectBamChipseq_4ae1abd1e8ef541bcd8db811bf3ed886.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-selectBamChipseq_4ae1abd1e8ef541bcd8db811bf3ed886.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-selectBamChipseq_4ae1abd1e8ef541bcd8db811bf3ed886.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-visualizeFeatureComb_c1b52f2815b4cfb70835cfe5cd69d51a.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-visualizeFeatureComb_c1b52f2815b4cfb70835cfe5cd69d51a.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-visualizeFeatureComb_c1b52f2815b4cfb70835cfe5cd69d51a.rdx
setting up git-svn bridge
Revision: 97035
Author: l.collado-torres
Date: 2014-11-22T22:10:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/R/annotateRegions.R
Modified  /trunk/madman/Rpacks/derfinder/man/annotateRegions.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 24f9fbb6f7979ad0f18f080b6c2b1249f8ea64e7

    Clarify doc for annotateRegions()

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-22 17:09:55 -0500
Author date: 2014-11-22 17:09:55 -0500
Revision: 97032
Author: l.collado-torres
Date: 2014-11-22T22:02:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/NEWS
Modified  /trunk/madman/Rpacks/derfinder/R/analyzeChr.R
Modified  /trunk/madman/Rpacks/derfinder/R/annotateRegions.R
Modified  /trunk/madman/Rpacks/derfinder/R/calculatePvalues.R
Modified  /trunk/madman/Rpacks/derfinder/R/calculateStats.R
Modified  /trunk/madman/Rpacks/derfinder/R/findRegions.R
Modified  /trunk/madman/Rpacks/derfinder/R/makeGenomicState.R
Modified  /trunk/madman/Rpacks/derfinder/R/mergeResults.R
Modified  /trunk/madman/Rpacks/derfinder/README.md
Modified  /trunk/madman/Rpacks/derfinder/inst/CITATION
Modified  /trunk/madman/Rpacks/derfinder/man/analyzeChr.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/annotateRegions.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/calculatePvalues.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/calculateStats.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/findRegions.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/makeGenomicState.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/mergeResults.Rd
Added  /trunk/madman/Rpacks/derfinder/tests/testthat/test_Fstats.R
Added  /trunk/madman/Rpacks/derfinder/tests/testthat/test_annotation.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_data.R
Added  /trunk/madman/Rpacks/derfinder/tests/testthat/test_findRegions.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_misc.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 30ede08171cc97c98b4a8dd6db0e27d50dd0f587

    v1.1.14 -- fix an important bug in calculatePvalues()

    This commit includes tests so that all functions in derfinder are now tested.
    Thus, in the future it will be easier to catch any bug introduced by
    changing the code.

    What prompted us to do this was a bug identified by reproducing results from
    version 0.0.63. The cause of the bug ended up being an incorrectly set value
    for the maxRegionGap parameter inside calculatePvalues(). It was set to 300
    instead of 0, meaning that the segments of base pairs passing the data filter
    were incorrectly grouped as findRegions() did have the correct default value of
    0.

    If you have results from prior to this fix, you could fix your regions using
    https://gist.github.com/bf85e2c7d5d1f8197707 However, note that the p-values
    will be approximated as there is no way to fix the null areas. If you want the
    correct p-values the only option is to re-run derfinder.

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-22 16:57:40 -0500
Author date: 2014-11-22 16:57:40 -0500
Revision: 97031
Author: bcarvalh
Date: 2014-11-22T15:06:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/pdInfoBuilder/R/pdBuilderV2HTA2.R
Modified  /trunk/madman/Rpacks/pdInfoBuilder/R/pdBuilderV2miRNA.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: a39a771ce6d1391f519434530721f0e40fae1bb7

    Merge pull request #4 from jmacdon/master

    Changes to accommodate Mouse Transcriptome 1.0 arrays
Committed by: Benilton Carvalho
Author Name: Benilton Carvalho
Commit date: 2014-11-22 13:06:45 -0200
Author date: 2014-11-22 13:06:45 -0200

Commit id: 640047735f3ee666da609f0bcf8e82c240bd691d

    Changes to accommodate Mouse Transcriptome 1.0 arrays

Committed by: Jim MacDonald
Author Name: Jim MacDonald
Commit date: 2014-11-21 14:02:56 -0800
Author date: 2014-11-21 14:02:56 -0800
Revision: 97028
Author: m.jiang
Date: 2014-11-22T00:39:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 97027
Author: m.carlson
Date: 2014-11-22T00:36:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/vignettes/AnnotationDbi.Rnw
Modified  /trunk/madman/Rpacks/AnnotationDbi/vignettes/IntroToAnnotationPackages.Rnw
Updates vignette to no longer use SweaveOpts
Revision: 97024
Author: s.arora
Date: 2014-11-21T23:02:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/R/recommendBiocViews.R
code update

- expt data packages do not have man pages or vignettes
- so modify code to recommend biocViews for packages
which do not have man pages or vignettes
Revision: 97022
Author: sdurinck
Date: 2014-11-21T21:59:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/biomaRt/DESCRIPTION
Modified  /trunk/madman/Rpacks/biomaRt/R/biomaRt.R
update of listEnsembl and useEnsembl functions. changed funcgen to regulation
Revision: 97021
Author: v.obenchain
Date: 2014-11-21T21:10:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
edit bpiterate() example re: number of available cores
Revision: 97019
Author: hpages
Date: 2014-11-21T20:05:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
Optimize strategy for preprocessing input of "findOverlaps" method for
GenomicRanges objects when 'algorithm' is "nclist".
Revision: 97018
Author: hpages
Date: 2014-11-21T19:56:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
improve NCLists_find_overlaps_and_combine()
Revision: 97016
Author: stvjc
Date: 2014-11-21T19:12:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLbase/R/storeFuncs.R
Modified  /trunk/madman/Rpacks/gQTLbase/R/storeS4.R
Modified  /trunk/madman/Rpacks/gQTLbase/vignettes/gqtlBase.Rmd
fixes to vignette
Revision: 97014
Author: f.marini
Date: 2014-11-21T18:42:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowcatchR/R/auxiliary.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c6e03c3528992c3112193c270db1c5d709ee8a75

    fixed behaviour in select.Frames when selecting a single frame

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 19:35:28 +0100
Author date: 2014-11-21 19:35:28 +0100
Revision: 97012
Author: f.marini
Date: 2014-11-21T17:10:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowcatchR/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowcatchR/NEWS
Modified  /trunk/madman/Rpacks/flowcatchR/R/preprocessing.R
Modified  /trunk/madman/Rpacks/flowcatchR/README.md
Modified  /trunk/madman/Rpacks/flowcatchR/vignettes/flowcatchR-vignette.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commits.

Commit information:

Commit id: cd7d031049a9413c13bfada96de491d97f31cd78

    added couple of info in readme.md for suggesting developments

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 18:09:52 +0100
Author date: 2014-11-21 18:09:52 +0100

Commit id: 34c43f9ce319000886768d1c2eb221aadfab44ff

    release version 1.0.1

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 18:02:42 +0100
Author date: 2014-11-21 18:02:42 +0100

Commit id: f8ab7fe7f437d7787a722dcb88b2d7b0fe6bee46

    reset version in DESCRIPTION before creating the git svn bridge for bioconductor

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 17:29:13 +0100
Author date: 2014-11-21 17:29:13 +0100

Commit id: 6d0482037cf0056d8428facd89796afe6c12a3b4

    fixed parameters name in the vignettes

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 16:13:26 +0100
Author date: 2014-11-21 16:13:26 +0100

Commit id: 328eb3a051a80e205fb8833b027d6bc2c48e3c0a

    placeholder for a todo set in the preprocessing

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-18 17:56:50 +0100
Author date: 2014-11-18 17:56:50 +0100
Revision: 97009
Author: l.gatto
Date: 2014-11-21T16:40:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/synapter/DESCRIPTION
Modified  /trunk/madman/Rpacks/synapter/NAMESPACE
Modified  /trunk/madman/Rpacks/synapter/NEWS
Modified  /trunk/madman/Rpacks/synapter/R/gui.R
Modified  /trunk/madman/Rpacks/synapter/README.md
Merge branch 'master' into local-hedgehog
Revision: 97008
Author: f.comoglio
Date: 2014-11-21T16:33:49+00:00
Paths:
Added  /trunk/madman/Rpacks/wavClusteR/DESCRIPTION
Added  /trunk/madman/Rpacks/wavClusteR/NAMESPACE
Added  /trunk/madman/Rpacks/wavClusteR/R/FDRbyRSF.R
Added  /trunk/madman/Rpacks/wavClusteR/R/annotateClusters.R
Added  /trunk/madman/Rpacks/wavClusteR/R/export.R
Added  /trunk/madman/Rpacks/wavClusteR/R/filterClusters.R
Added  /trunk/madman/Rpacks/wavClusteR/R/fitMixtureModel.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getAllSub.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getClusters.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getExpInterval.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getHighConfSub.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getMeta.R
Added  /trunk/madman/Rpacks/wavClusteR/R/plotSizeDistribution.R
Added  /trunk/madman/Rpacks/wavClusteR/R/plotStatistics.R
Added  /trunk/madman/Rpacks/wavClusteR/R/plotSubstitutions.R
Added  /trunk/madman/Rpacks/wavClusteR/R/processMD.R
Added  /trunk/madman/Rpacks/wavClusteR/R/readSortedBam.R
Added  /trunk/madman/Rpacks/wavClusteR/R/wavCWTPeaksCF.R
Added  /trunk/madman/Rpacks/wavClusteR/README.md
Added  /trunk/madman/Rpacks/wavClusteR/inst/CITATION
Added  /trunk/madman/Rpacks/wavClusteR/inst/extdata/example.bam
Added  /trunk/madman/Rpacks/wavClusteR/inst/extdata/example.bam.bai
Added  /trunk/madman/Rpacks/wavClusteR/man/FitMixtureModel.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/annotateClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/estimateFDR.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportCoverage.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportHighConfSub.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportSequences.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/filterClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getAllSub.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getExpInterval.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getHighConfSub.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getMetaCoverage.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getMetaGene.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getMetaTSS.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/model.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/plotSizeDistribution.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/plotStatistics.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/plotSubstitutions.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/readSortedBam.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/wavClusteR-package.Rd
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/AGO2annotation.pdf
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/AGO2metagene.pdf
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/wavCluster_vignette.Rnw
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/wavCluster_vignette.pdf
Added  /trunk/madman/Rpacks/wavClusteR/wavClusteR_1.99.0.tar.gz
Added  /trunk/madman/Rpacks/wavClusteR/wavClusteR_1.99.1.tar.gz
Added  /trunk/madman/Rpacks/wavClusteR/wavClusteR_1.99.2.tar.gz
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 52ac07b205705bbf15b83c59774e0df0784c95ee

    pushing changed to GitHub, to become effective via GH-SVN bridge.

Committed by: FC
Author Name: FC
Commit date: 2014-11-21 17:33:18 +0100
Author date: 2014-11-21 17:33:18 +0100
Revision: 97006
Author: l.collado-torres
Date: 2014-11-21T16:10:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderPlot/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c370d50a56f886be22e6befbc03f0c318c79277f

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:10:06 -0500
Author date: 2014-11-21 11:10:06 -0500
Revision: 97005
Author: l.collado-torres
Date: 2014-11-21T16:09:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/.travis.yml
Modified  /trunk/madman/Rpacks/derfinder/R/findRegions.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 16acd6866ded1115c35a611cbd4ac93e48c6cd91

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:09:11 -0500
Author date: 2014-11-21 11:09:11 -0500
Revision: 97004
Author: l.collado-torres
Date: 2014-11-21T16:08:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: cdcb65041b66ca6915e6b0018329804637f535db

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:08:55 -0500
Author date: 2014-11-21 11:08:55 -0500
Revision: 97003
Author: l.collado-torres
Date: 2014-11-21T16:08:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderHelper/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 9f21311b355ed3576956bba8a3b8164dff76e674

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:08:36 -0500
Author date: 2014-11-21 11:08:36 -0500
Revision: 97002
Author: z.ji
Date: 2014-11-21T13:57:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/inst/shiny/ui.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 13c0367b2254180e046d0c5e5d39dfc97de242a6

    Merge branch 'master' of https://github.com/zji90/GSCA

    Conflicts:
        inst/shiny/ui.R

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-21 08:57:13 -0500
Author date: 2014-11-21 08:57:13 -0500

Commit id: 867060d17e58c4d185763f6a784aa33206119c80

    Changed UI appearances

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-12 14:21:53 -0500
Author date: 2014-11-12 14:21:53 -0500
Revision: 97001
Author: z.ji
Date: 2014-11-21T13:56:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/TSCAN/R/TSCANorder.R
Modified  /trunk/madman/Rpacks/TSCAN/R/exprmclust.R
Modified  /trunk/madman/Rpacks/TSCAN/R/plotmclust.R
Modified  /trunk/madman/Rpacks/TSCAN/inst/shiny/server.R
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/shinyapps
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/shinyapps/zhiji
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/shinyapps/zhiji/TSCAN.dcf
Modified  /trunk/madman/Rpacks/TSCAN/inst/shiny/ui.R
Modified  /trunk/madman/Rpacks/TSCAN/man/TSCANorder.Rd
Modified  /trunk/madman/Rpacks/TSCAN/man/exprmclust.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 1b2d331b30c6dd414b348496bd7d826a50c600b7

    updating UI

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-21 08:56:49 -0500
Author date: 2014-11-21 08:56:49 -0500

Commit id: 3c5f9502984e7c3b2da5b8e8f3b3d90f2b9900ca

    Revised TSCANorder func to report multiple branches

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-12 14:21:41 -0500
Author date: 2014-11-12 14:21:41 -0500
Revision: 96997
Author: b.knapp
Date: 2014-11-21T07:50:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/NAMESPACE
update pacakge for the use with time series
Revision: 96996
Author: b.knapp
Date: 2014-11-21T07:48:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/NAMESPACE
update pacakge for the use with time series
Revision: 96995
Author: b.knapp
Date: 2014-11-21T07:42:31+00:00
Paths:
Added  /trunk/madman/Rpacks/lpNet/man/generateTimeSeriesNetStates.Rd
Added  /trunk/madman/Rpacks/lpNet/man/getBaseline.Rd
add manuals
Revision: 96993
Author: b.knapp
Date: 2014-11-21T07:39:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/DESCRIPTION
update of lpNet for the use with time series data
Revision: 96992
Author: hpages
Date: 2014-11-21T07:38:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Speed up findOverlaps_GNCList() by taking advantage of latest
IRanges:::NCLists_find_overlaps_and_combine() improvements.
Revision: 96991
Author: hpages
Date: 2014-11-21T07:35:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Add 'select' arg to NCLists_find_overlaps_and_combine(). Hit selection is
entirely done in C.
Revision: 96990
Author: b.knapp
Date: 2014-11-21T07:26:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/DESCRIPTION
update of lpNet for the use with time series data
Revision: 96989
Author: hpages
Date: 2014-11-21T07:14:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
NCLists_find_overlaps_and_combine() now handles the space of the ranges at the
C level. This will be used by GenomicRanges:::findOverlaps_GNCList() to handle
the ignore.strand=FALSE case more efficiently.
Revision: 96988
Author: d.strbenac
Date: 2014-11-21T07:00:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/rankPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/man/selectionPlot.Rd
Preserve order of levels appearing in results list for rankPlot and selectionPlot.
Revision: 96986
Author: s.xu
Date: 2014-11-21T04:21:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/sapFinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/sapFinder/inst/NEWS
Modified  /trunk/madman/Rpacks/sapFinder/inst/parser4sapFinder.jar
To modify FDR method
Revision: 96985
Author: hpages
Date: 2014-11-21T03:38:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Add more tests for when the input of NCList() and findOverlaps_NCList() is on a
circular space.
Revision: 96984
Author: j.maksimovic
Date: 2014-11-21T02:58:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/DESCRIPTION
Modified  /trunk/madman/Rpacks/missMethyl/vignettes/missMethyl.Rnw
Made change in vignette to deal with minfi bug fix in read.450k.exp. Path should now be correctly constructed when a targets file is included.
Revision: 96983
Author: hpages
Date: 2014-11-21T01:53:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Add tests for when the input of NCList() and findOverlaps_NCList() are ranges
on a circular space.
Revision: 96982
Author: m.carlson
Date: 2014-11-21T00:57:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/vignettes/IntroToAnnotationPackages.Rnw
Mentions mapIds in the vignette
Revision: 96981
Author: m.carlson
Date: 2014-11-21T00:53:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/safe/DESCRIPTION
Modified  /trunk/madman/Rpacks/safe/R/safe.toptable.R
Bug fix to safe.toptable function.

Replaces a call to mget with a call to mapIds
Revision: 96980
Author: m.carlson
Date: 2014-11-20T23:59:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/man/AnnotationDb-class.Rd
Better description of many to one relationships in the manual page.
Revision: 96979
Author: m.carlson
Date: 2014-11-20T23:40:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/inst/unitTests/test_mapIds.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/man/AnnotationDb-class.Rd
Modified  /trunk/madman/Rpacks/AnnotationDbi/man/Bimap-envirAPI.Rd
Documents mapIds function and removes warnings about 1:many mappings
Revision: 96978
Author: r.castelo
Date: 2014-11-20T23:09:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/commonFunctions.R
Fixed .cDNAloc()
Revision: 96976
Author: d.strbenac
Date: 2014-11-20T23:00:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/rankPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Commonality plots now work for a comparison factor with three or more levels.
Revision: 96975
Author: m.carlson
Date: 2014-11-20T22:13:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
Added  /trunk/madman/Rpacks/AnnotationDbi/inst/unitTests/test_mapIds.R
Adds unit tests and makes behavior for mapIds more consistent.
Revision: 96974
Author: a.lun
Date: 2014-11-20T22:04:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Added Aaron to maintainer list.
Revision: 96973
Author: stvjc
Date: 2014-11-20T21:30:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/parody/DESCRIPTION
testing from rex2
Revision: 96972
Author: stvjc
Date: 2014-11-20T21:10:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/parody/DESCRIPTION
testing svn write priv
Revision: 96971
Author: hpages
Date: 2014-11-20T21:06:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
fix bug in C code behind findOverlaps_NCList(), findOverlaps_NCLists(), and
NCLists_find_overlaps_and_combine()
Revision: 96970
Author: hpages
Date: 2014-11-20T20:44:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
GNCList() and findOverlaps_GNCList() now support circular underlying sequences
Revision: 96969
Author: hpages
Date: 2014-11-20T20:41:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
NCList now support ranges on circular spaces
Revision: 96968
Author: d.tenenbaum
Date: 2014-11-20T20:04:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/PICS/DESCRIPTION
Modified  /trunk/madman/Rpacks/PICS/NAMESPACE
Modified  /trunk/madman/Rpacks/PING/DESCRIPTION
Modified  /trunk/madman/Rpacks/PING/NAMESPACE
NAMESPACE tweaks
Revision: 96967
Author: m.carlson
Date: 2014-11-20T19:15:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
More tidying for code that gets a new DB

Also makes sure that the new DB is valid
Revision: 96965
Author: v.obenchain
Date: 2014-11-20T18:59:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/vignettes/IntroductionToBiocParallel.Rnw
add note to vignette re: module load in template file
Revision: 96964
Author: d.tenenbaum
Date: 2014-11-20T18:55:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
safer transfer of highest id
Revision: 96963
Author: stvjc
Date: 2014-11-20T18:17:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/parody/DESCRIPTION
testing from rex
Revision: 96962
Author: hpages
Date: 2014-11-20T17:28:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
minor simplification
Revision: 96959
Author: hpages
Date: 2014-11-20T11:52:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Another findOverlaps_GNCList() speedup by using new
IRanges:::NCLists_find_overlaps_and_combine() instead of
IRanges:::findOverlaps_NCLists().
Revision: 96958
Author: hpages
Date: 2014-11-20T11:47:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Add NCLists_find_overlaps_and_combine() (non-exported) as the new workhorse
behind GenomicRanges:::findOverlaps_GNCList().
Revision: 96957
Author: hpages
Date: 2014-11-20T09:31:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
tidy up code
Revision: 96955
Author: d.strbenac
Date: 2014-11-20T06:00:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Added  /trunk/madman/Rpacks/ClassifyR/R/rankPlot.R
Deleted  /trunk/madman/Rpacks/ClassifyR/R/rankStabilityPlot.R
Added  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Added  /trunk/madman/Rpacks/ClassifyR/man/rankPlot.Rd
Deleted  /trunk/madman/Rpacks/ClassifyR/man/rankStabilityPlot.Rd
Added  /trunk/madman/Rpacks/ClassifyR/man/selectionPlot.Rd
rankStabilityPlot changed to rankPlot. Now does both stability and commonality between analyses. More options for plot margins and labels.
Revision: 96954
Author: hpages
Date: 2014-11-20T05:33:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
more work on internal helper NCLists_find_overlaps()
Revision: 96952
Author: l.collado-torres
Date: 2014-11-20T05:10:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/README.md
Modified  /trunk/madman/Rpacks/derfinder/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6160296c8d23459d5a623bae8a7baa9f60f83a4b

    Update version in citation

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-20 00:10:48 -0500
Author date: 2014-11-20 00:10:48 -0500
Revision: 96951
Author: l.collado-torres
Date: 2014-11-20T05:08:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/R/coverageToExon.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e13416de9257101d21fbc31a1e02023870950b15

    Don't need library() and ::: for coverageToExon() as revealed by R CMD check with and without them

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-20 00:08:38 -0500
Author date: 2014-11-20 00:08:38 -0500
Revision: 96950
Author: l.collado-torres
Date: 2014-11-20T04:50:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/R/coverageToExon.R
Modified  /trunk/madman/Rpacks/derfinder/R/fullCoverage.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_data.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ca2e02cac0d004e31a0b5e2801f71311d4f0a37f

    v1.1.13 -- fixed coverageToExon() use with multiple cores. Testing if ::: is needed

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-19 23:49:52 -0500
Author date: 2014-11-19 23:49:52 -0500
Revision: 96948
Author: v.obenchain
Date: 2014-11-20T02:43:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/R/MulticoreParam-class.R
Modified  /trunk/madman/Rpacks/BiocParallel/inst/unitTests/test_bpiterate.R
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
modify bpiterate() man pages example for windows
Revision: 96947
Author: hpages
Date: 2014-11-20T02:41:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/GAlignmentPairs-class.R
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/GAlignments-class.R
internal utility makeClassinfoRowForCompactPrinting() is now in S4Vectors
Revision: 96946
Author: hpages
Date: 2014-11-20T02:38:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/BSgenomeViews-class.R
internal utility makeClassinfoRowForCompactPrinting() is now in S4Vectors
Revision: 96945
Author: hpages
Date: 2014-11-20T02:36:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/utils.R
internal utility makeClassinfoRowForCompactPrinting() is now in S4Vectors
Revision: 96944
Author: n.malani
Date: 2014-11-20T02:36:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/hiAnnotator/DESCRIPTION
Modified  /trunk/madman/Rpacks/hiAnnotator/NEWS
Modified  /trunk/madman/Rpacks/hiAnnotator/R/hiAnnotator.R
added allSubjectCols & overlapType params to getSitesInFeature
Revision: 96943
Author: smyth
Date: 2014-11-20T02:34:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/plotMDS.DGEList.R
Modified  /trunk/madman/Rpacks/edgeR/man/glmfit.Rd
Modified  /trunk/madman/Rpacks/edgeR/man/plotMDS.DGEList.Rd
plotMDS.DGEList now has argument pch and col argument is removed.
Revision: 96942
Author: v.obenchain
Date: 2014-11-20T02:31:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/mapCoords-methods.R
add .listCumsumShifted() helper back
Revision: 96941
Author: hpages
Date: 2014-11-20T02:29:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/Hits-class-leftovers.R
Remove old and sluggish "show" method for Hits object (there is now a fast
method in S4Vectors that produces output with a more ``modern'' look).
Revision: 96940
Author: hpages
Date: 2014-11-20T02:17:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/R/Hits-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/utils.R
Modified  /trunk/madman/Rpacks/S4Vectors/man/Hits-class.Rd
Add ``modern'' "show" method for Hits objects (will become effective when old
and sluggish method defined in IRanges is removed).
Revision: 96939
Author: m.carlson
Date: 2014-11-20T01:21:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
Fixes bug that was remaining disconnected to older DB.
Revision: 96938
Author: m.carlson
Date: 2014-11-20T00:59:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
fixes tricky bug that sometimes looked at wrong online resource for the 'highest id'
Revision: 96937
Author: mtmorgan
Date: 2014-11-20T00:52:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeUCSCChain.R
minor makeUCSC* cleanup

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