Subversion Logs

This is a list of recent commits to the development branch of the Bioconductor Subversion repository.

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Revision: 113522
Author: l.chavez
Date: 2016-02-11T12:09:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.correlation.R
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.selectROIs.R
Modified  /trunk/madman/Rpacks/MEDIPS/man/MEDIPS.correlation.Rd
Modified  /trunk/madman/Rpacks/MEDIPS/man/MEDIPS.selectROIs.Rd
sum addeded to MEDIPS.selectROI
Revision: 113520
Author: hpages
Date: 2016-02-11T11:13:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/inter-range-methods.R
clean up long-standing messy code in inter-range-methods.R
Revision: 113519
Author: v.kiselev
Date: 2016-02-11T09:58:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/SC3/DESCRIPTION
Modified  /trunk/madman/Rpacks/SC3/R/sc3-funcs.R
Modified  /trunk/madman/Rpacks/SC3/R/sc3.R
Modified  /trunk/madman/Rpacks/SC3/man/sc3.Rd
fix bug when running SC3 on a data.frame, now it coverts it to a matrix first
Revision: 113517
Author: m.choi
Date: 2016-02-11T03:50:09+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MSstats/R/mainfunctions.R
deleting a file
Revision: 113513
Author: smyth
Date: 2016-02-11T01:49:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/R/kegga.R
Modified  /trunk/madman/Rpacks/limma/R/voom.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/propexpr.Rd
Modified  /trunk/madman/Rpacks/limma/man/voom.Rd
11 February 2016: limma 3.27.12

- new argument 'save.plot' for voom().

- bug fix for kegga() when 'covariate' or 'prior.prob' are not NULL
  and when not all genes in the universe have annotation.
Revision: 113510
Author: a.popa
Date: 2016-02-10T22:14:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/RiboProfiling/DESCRIPTION
Modified  /trunk/madman/Rpacks/RiboProfiling/NEWS
Modified  /trunk/madman/Rpacks/RiboProfiling/R/aroundPromoter.R
Modified  /trunk/madman/Rpacks/RiboProfiling/R/riboSeqFromBAM.R
Modified  /trunk/madman/Rpacks/RiboProfiling/man/riboSeqFromBAM.Rd
SummarizedExperiment::assay
added parameter paramScanBAM (ScanBamParam object) to riboSeqFromBAM function
Revision: 113508
Author: hpages
Date: 2016-02-10T22:07:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/extractTranscriptSeqs.Rd
Try to be even more explicit about ordering of exons passed to
extractTranscriptSeqs().
Revision: 113506
Author: j.java
Date: 2016-02-10T20:07:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Fixed tracker-summary problem; version bump
Revision: 113505
Author: hpages
Date: 2016-02-10T19:38:59+00:00
Paths:
Added  /trunk/madman/Rpacks/HDF5Array
Added  /trunk/madman/Rpacks/HDF5Array/DESCRIPTION
start HDF5Array package
Revision: 113504
Author: hpages
Date: 2016-02-10T19:22:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/man/SNPlocs-class.Rd
small code simplification
Revision: 113503
Author: hpages
Date: 2016-02-10T19:04:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
minor rephrasing
Revision: 113502
Author: hpages
Date: 2016-02-10T18:59:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Coercion from GenomicRanges to GPos now propagates the metadata columns.
Also now it emits a warning when the names on the object to coerce are not
propagated.
Revision: 113501
Author: hpages
Date: 2016-02-10T18:33:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
minor edit
Revision: 113500
Author: hpages
Date: 2016-02-10T18:24:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
add coercion from GenomicRanges to GPos
Revision: 113499
Author: m.mccall
Date: 2016-02-10T18:06:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/spkTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/spkTools/R/spkPair.R
Deleted  /trunk/madman/Rpacks/spkTools/inst
Fix array dimnames error in spkPair function.
Revision: 113496
Author: t.silva
Date: 2016-02-10T17:39:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/NAMESPACE
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAInternal.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAPrepare.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAbiolinks.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAvisualize.R
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/batch.info.Rd
Deleted  /trunk/madman/Rpacks/TCGAbiolinks/man/batchinfo.Rd
Merge branch 'master' into devel

* master:
  jittrValueLabels was removed from sjplot. Importing grid library was conflicting with cowlplot import.
  This closes #6. It shoud be verified if there are columns with different names but same content.
  Correting the name of the object. This should remove the warning from bioconductor.
  Version bump
  Bug fix: This closes #5

From: tiago <tiagochst@gmail.com>
Revision: 113495
Author: v.obenchain
Date: 2016-02-10T17:17:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/rpx/DESCRIPTION
Modified  /trunk/madman/Rpacks/rpx/vignettes/rpx.Rnw
remove duplicate code in vignette
Revision: 113494
Author: z.skidmore
Date: 2016-02-10T17:15:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenVisR/DESCRIPTION
bump version
Revision: 113493
Author: z.skidmore
Date: 2016-02-10T17:13:00+00:00
Paths:
 /trunk/madman/Rpacks/GenVisR/DESCRIPTION
Deleted  /trunk/madman/Rpacks/GenVisR/Images
 /trunk/madman/Rpacks/GenVisR/LICENSE
 /trunk/madman/Rpacks/GenVisR/NAMESPACE
 /trunk/madman/Rpacks/GenVisR/NEWS
 /trunk/madman/Rpacks/GenVisR/R
Added  /trunk/madman/Rpacks/GenVisR/R/GenVisR.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_alignPlot.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_annoTransTranv.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_calcTransTranvFreq.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_convMaf.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_rmIndel.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_rmMnuc.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnFreq.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnFreq_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnFreq_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnSpec.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnSpec_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnSpec_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_align.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_subsetChr.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_bamRcnt.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_bamRcnt_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_format.R
Added  /trunk/madman/Rpacks/GenVisR/R/covBars.R
Added  /trunk/madman/Rpacks/GenVisR/R/covBars_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/covBars_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_alignPlot.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_assign_ggplotGrob_height.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_assign_ggplotGrob_width.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_buildCov.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_buildTrack.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_extr_ggplotGrob_height.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_extr_ggplotGrob_width.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_trackViz.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_Granges2dataframe.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_buildGene.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_calcGC.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_cdsFromTXID.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_extrCDS.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_extrUTR.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_formatUTR.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_formatcds.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mapCoordSpace.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mapCovCoordSpace.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mergeRegions.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mergeTypeRegions.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mergeTypes.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView_formatCytobands.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_fileGlob.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_lohCalc.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_slidingWindow.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_stepCalc.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_tileCalc.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_tilePosition.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_tileWindow.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_windowPosition.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_AA2sidechain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_Codon2AA.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_DNAconv.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_constructGene.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_dodgeCoordX.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_dodgeCoordY.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_fetchDomain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_mutationObs.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_reduceLolli.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_transcriptID2codingSeq.R
Added  /trunk/madman/Rpacks/GenVisR/R/multi_buildClin.R
Added  /trunk/madman/Rpacks/GenVisR/R/multi_chrBound.R
Added  /trunk/madman/Rpacks/GenVisR/R/multi_cytobandRet.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_Custom2anno.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_MAF2anno.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_MGI2anno.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_NA2gene.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_align.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildGenePrevelance.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildMutBurden_A.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildMutBurden_B.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_calcMutFreq.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_geneAlt.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_geneRecurCutoff.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_geneSort.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_hierarchyTRV.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_rmvSilent.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_sampAlt.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_sampSort.R
 /trunk/madman/Rpacks/GenVisR/README.md
Deleted  /trunk/madman/Rpacks/GenVisR/Test_data
 /trunk/madman/Rpacks/GenVisR/data
Added  /trunk/madman/Rpacks/GenVisR/data/HCC1395_Germline.rda
Added  /trunk/madman/Rpacks/GenVisR/data/HCC1395_N.rda
Added  /trunk/madman/Rpacks/GenVisR/data/HCC1395_T.rda
Added  /trunk/madman/Rpacks/GenVisR/data/LucCNseg.rda
Added  /trunk/madman/Rpacks/GenVisR/data/SNPloci.rda
Added  /trunk/madman/Rpacks/GenVisR/data/brcaMAF.rda
Added  /trunk/madman/Rpacks/GenVisR/data/cytoGeno.rda
Added  /trunk/madman/Rpacks/GenVisR/data/hg19chr.rda
Deleted  /trunk/madman/Rpacks/GenVisR/inst
 /trunk/madman/Rpacks/GenVisR/man
Added  /trunk/madman/Rpacks/GenVisR/man/GenVisR.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/HCC1395_Germline.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/HCC1395_N.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/HCC1395_T.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/LucCNseg.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/SNPloci.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_alignPlot.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_annoTransTranv.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_calcTransTranvFreq.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_convMAF.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_rmIndel.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_rmMnuc.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/brcaMAF.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnFreq.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnFreq_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnFreq_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnSpec.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnSpec_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnSpec_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnView.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnView_align.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnView_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnView_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cnView_subsetChr.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/compIdent.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/compIdent_bamRcnt.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/compIdent_bamRcnt_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/compIdent_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/compIdent_format.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/covBars.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/covBars_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/covBars_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/cytoGeno.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_alignPlot.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_assign_ggplotGrob_height.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_assign_ggplotGrob_width.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_buildCov.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_buildTrack.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_extr_ggplotGrob_height.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_extr_ggplotGrob_width.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/genCov_trackViz.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_Granges2dataframe.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_buildGene.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_calcGC.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_cdsFromTXID.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_extrCDS.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_extrUTR.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_formatCDS.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_formatUTR.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_mapCoordSpace.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_mapCovCoordSpace.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_mergeRegions.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_mergeTypeRegions.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/geneViz_mergeTypes.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/hg19chr.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/ideoView.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/ideoView_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/ideoView_formatCytobands.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/ideoView_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_fileGlob.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_lohCalc.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_slidingWindow.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_stepCalc.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_tileCalc.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_tilePosition.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_tileWindow.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lohView_windowPosition.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_AA2sidechain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_Codon2AA.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_DNAconv.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_constructGene.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_dodgeCoordX.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_dodgeCoordY.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_fetchDomain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_mutationObs.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_reduceLolli.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/lolliplot_transcriptID2codingSeq.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/multi_buildClin.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/multi_chrBound.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/multi_cytobandRet.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_Custom2anno.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_MAF2anno.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_MGI2anno.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_NA2gene.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_align.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_buildGenePrevelance.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_buildMain.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_buildMutBurden_A.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_buildMutBurden_B.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_calcMutFreq.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_geneAlt.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_geneRecurCutoff.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_geneSort.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_hierarchyTRV.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_qual.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_rmvSilent.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_sampAlt.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/waterfall_sampSort.Rd
 /trunk/madman/Rpacks/GenVisR/tests
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-TvTi.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-TvTi_calcTransTranvFreq.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-TvTi_convMaf.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-TvTi_qual.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-TvTi_rmIndel.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-TvTi_rmMnuc.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-cnSpec.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-cnSpec_qual.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-cnView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-cnView_subsetChr.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-genCov_qual.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-ideoView_formatCytobands.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_AA2sidechain.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_Codon2AA.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_DNAconv.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_constructGene.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_dodgeCoordX.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_dodgeCoordY.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_mutationObs.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_qual.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-lolliplot_reduceLolli.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-multi_chrBound.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-multi_cytobandRet.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_MAF2anno.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_MGI2anno.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_NA2gene.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_calcMutFreq.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_geneAlt.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_geneRecurCutoff.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_geneSort.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_qual.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_rmvSilent.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_sampAlt.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test-waterfall_sampSort.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat/test_waterfall_hierarchyTRV.R
Added  /trunk/madman/Rpacks/GenVisR/tests/testthat.R
 /trunk/madman/Rpacks/GenVisR/vignettes
Added  /trunk/madman/Rpacks/GenVisR/vignettes/GenVisR_intro.Rmd
attempt sync with github
Revision: 113489
Author: a.reyes
Date: 2016-02-10T10:37:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEXSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/DEXSeq/R/visualization.R
support for NA's in transcripts field for plotDEXSeq
Revision: 113488
Author: hpages
Date: 2016-02-10T10:15:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
credit Juri Stricker and Julien Gagneur for the ideas behind GPos
Revision: 113487
Author: hpages
Date: 2016-02-10T09:50:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/inter-range-methods.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/inter-range-methods.Rd
Add a seqinfo() setter for GPos objects. This single addition enables the
following:
  - the family of setters that operate on the seqinfo component of an object
    (seqlevels(), seqlengths(), isCircular(), and genome())
  - pcompare() and all the binary comparison operators (==, <=, !=, >=, <, >)
Revision: 113486
Author: v.kiselev
Date: 2016-02-10T09:37:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/SC3/DESCRIPTION
Modified  /trunk/madman/Rpacks/SC3/R/sc3.R
Modified  /trunk/madman/Rpacks/SC3/man/sc3.Rd
add gene.filter and log.scale boolean parameters to sc3() to be able to run it on filtered/scaled datasets, e.g. patel
Revision: 113484
Author: hpages
Date: 2016-02-10T08:01:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GRanges-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/DelegatingGenomicRanges-class.Rd
Try to be more systematic when choosing between update(), clone(), and
BiocGenerics:::replaceSlots() in the various methods for GenomicRanges or
GRanges objects that return a modified object (a.k.a. endomorphisms).
Revision: 113482
Author: v.obenchain
Date: 2016-02-10T04:09:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/man/summarizeOverlaps-methods.Rd
document BPPARAM arg to '...' for summarizeOverlaps()
Revision: 113481
Author: hpages
Date: 2016-02-10T03:24:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-comparison.R
one leftover from previous renaming
Revision: 113480
Author: hpages
Date: 2016-02-10T03:18:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
add GenomicRanges to Suggests field
Revision: 113478
Author: hpages
Date: 2016-02-10T02:42:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/NAMESPACE
Modified  /trunk/madman/Rpacks/S4Vectors/R/Rle-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/Rle-utils.R
Modified  /trunk/madman/Rpacks/S4Vectors/inst/unitTests/test_Rle-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/man/Rle-class.Rd
Some refactoring of the Rle() generic and methods:
- Remove ellipsis from the argument list of the generic.
- Dispatch on 'values' only.
- The 'values' and 'lengths' arguments now have explicit default values
  logical(0) and integer(0) respectively.
- Reduce set of methods from 5 to 2 without loss of functionality.
- Methods have no more 'check' argument but new low-level (non-exported)
  constructor new_Rle() does and is what should be used now by code that needs
  this feature.
Revision: 113476
Author: n.lawlor
Date: 2016-02-10T01:39:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/multiClust/vignettes/multiClust.Rmd
Added change to vignette for obtaining gene expression files. When using the getGEO() function you need to treat "gse" as a list. Therefore, the code should be:

data.gse <- exprs(gse[[1]])
Revision: 113475
Author: p.stempor
Date: 2016-02-10T01:17:20+00:00
Paths:
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui/FataTablesColumnSetup.js
Merge branch 'devel' of github.com:Przemol/seqplots into devel

From: Przemol 

Revision: 113474
Author: p.stempor
Date: 2016-02-10T01:15:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/.travis.yml
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqplots/NAMESPACE
Modified  /trunk/madman/Rpacks/seqplots/R/generic_methods.R
Modified  /trunk/madman/Rpacks/seqplots/R/getPlotSetArray.R
Modified  /trunk/madman/Rpacks/seqplots/R/plotHeatmap.R
Modified  /trunk/madman/Rpacks/seqplots/R/run.R
Modified  /trunk/madman/Rpacks/seqplots/R/seqplots-package.R
Modified  /trunk/madman/Rpacks/seqplots/README.md
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL/server_plotHeatmap.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/doFileOperations.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/mcCalcStart_calculations.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/mcDoParallel_plotting.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/global.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/server.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui/DataTablesColumnSetup.js
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui/FileManagementModal.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui/loadModal.html
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/style.css
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/Install_OSX.md
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/help.html
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/afterHTMLgridrender.js
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/color.js
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/js_addons.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/tutorial.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/outro.html
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/tutorial.html
Modified  /trunk/madman/Rpacks/seqplots/man/MotifSetup-class.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/PlotSetArray-class.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/PlotSetList-class.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/PlotSetPair-class.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/deployServerInstance.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/getPlotSetArray.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/ggHeatmapPlotWrapper.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/heatmapPlotWrapper.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/imPlot2.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/num2bp.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/num2sci.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/plot.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/plotAverage.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/plotHeatmap.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/plotMext.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/run.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/seqplots-generic.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/seqplots.Rd
Modified  /trunk/madman/Rpacks/seqplots/tests/testthat/test1.R
Merge branch 'master' into devel

* master: (637 commits)
  version set to devel
  Update README.md
  version bump
  docs updated for new SeqPlots OS X installation
  version bump
  simplified features and tracks tables (without redundant selection column), selection buttons and indicators rendered outside of table area
  version bump
  dropped date formatting, as it dosen't work properly in DT
  Deprecated dbBeginTransaction() changed to dbBegin()
  fix for "Construct labels using row and col fields" button, when >9 columns or rows are rendered
  version bump
  search Delay for DT reduced for better responsiveness
  added Remotes to DESCRIPTION for rstudio/DT (0.1.45, remote selection and DT proxy features)
  version bump
  fix for tutorial
  fix for track matching multiple seqnames style
  updated dependencies
  server side tracks/features selection with persistent selection
  server side DT
  version bump to 1.7.12
  ...

From: Przemol 

Revision: 113473
Author: p.stempor
Date: 2016-02-10T00:53:28+00:00
Paths:
Added  /trunk/madman/Rpacks/seqplots/README
readme added to index

From: przemol <pstempor@gmail.com>
Revision: 113472
Author: p.stempor
Date: 2016-02-10T00:53:15+00:00
Paths:
Added  /trunk/madman/Rpacks/seqplots/.project
Deleted  /trunk/madman/Rpacks/seqplots/SeqPlots/test.R
cleanup over https

From: przemol <pstempor@gmail.com>
Revision: 113471
Author: p.stempor
Date: 2016-02-10T00:53:01+00:00
Paths:
Added  /trunk/madman/Rpacks/seqplots/SeqPlots
Added  /trunk/madman/Rpacks/seqplots/SeqPlots/test.R
test

From: przemol <pstempor@gmail.com>
Revision: 113470
Author: p.stempor
Date: 2016-02-10T00:52:29+00:00
Paths:
Added  /trunk/madman/Rpacks/seqplots/functions
Added  /trunk/madman/Rpacks/seqplots/functions/calc.R
Added  /trunk/madman/Rpacks/seqplots/functions/calcAnchored.R
Added  /trunk/madman/Rpacks/seqplots/functions/calcMidpoints.R
Added  /trunk/madman/Rpacks/seqplots/functions/files_modal.R
Added  /trunk/madman/Rpacks/seqplots/functions/fnPlotHeatmap.R
Added  /trunk/madman/Rpacks/seqplots/functions/multicoreCalcStart.R
Added  /trunk/madman/Rpacks/seqplots/functions/plotMext.R
Added  /trunk/madman/Rpacks/seqplots/functions/procQuick.R
Added  /trunk/madman/Rpacks/seqplots/functions/procTSSsimple.R
Added  /trunk/madman/Rpacks/seqplots/functions/renderHTMLfilesGrid.R
Added  /trunk/madman/Rpacks/seqplots/functions/renderHTMLgrid.R
Added  /trunk/madman/Rpacks/seqplots/seqplots_dev.Rproj
Added  /trunk/madman/Rpacks/seqplots/server.R
Added  /trunk/madman/Rpacks/seqplots/ui.R
Added  /trunk/madman/Rpacks/seqplots/www
Added  /trunk/madman/Rpacks/seqplots/www/css
Added  /trunk/madman/Rpacks/seqplots/www/css/DT_bootstrap.css
Added  /trunk/madman/Rpacks/seqplots/www/css/NewFont.woff
Added  /trunk/madman/Rpacks/seqplots/www/css/TableTools.css
Added  /trunk/madman/Rpacks/seqplots/www/css/bootstrapSwitch.css
Added  /trunk/madman/Rpacks/seqplots/www/css/font-awesome.min.css
Added  /trunk/madman/Rpacks/seqplots/www/css/images
Added  /trunk/madman/Rpacks/seqplots/www/css/images/Sorting icons.psd
Added  /trunk/madman/Rpacks/seqplots/www/css/images/back_disabled.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/back_enabled.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/back_enabled_hover.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/favicon.ico
Added  /trunk/madman/Rpacks/seqplots/www/css/images/forward_disabled.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/forward_enabled.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/forward_enabled_hover.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/sort_asc.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/sort_asc_disabled.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/sort_both.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/sort_desc.png
Added  /trunk/madman/Rpacks/seqplots/www/css/images/sort_desc_disabled.png
Added  /trunk/madman/Rpacks/seqplots/www/css/mask2.png
Added  /trunk/madman/Rpacks/seqplots/www/css/nv.d3.css
Added  /trunk/madman/Rpacks/seqplots/www/css/rNVD3.css
Added  /trunk/madman/Rpacks/seqplots/www/css/style.css
Added  /trunk/madman/Rpacks/seqplots/www/font
Added  /trunk/madman/Rpacks/seqplots/www/font/FontAwesome.otf
Added  /trunk/madman/Rpacks/seqplots/www/font/fontawesome-webfont.eot
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Added  /trunk/madman/Rpacks/seqplots/www/font/fontawesome-webfont.ttf
Added  /trunk/madman/Rpacks/seqplots/www/font/fontawesome-webfont.woff
Added  /trunk/madman/Rpacks/seqplots/www/js
Added  /trunk/madman/Rpacks/seqplots/www/js/DT_bootstrap.js
Added  /trunk/madman/Rpacks/seqplots/www/js/DT_filter.js
Added  /trunk/madman/Rpacks/seqplots/www/js/TableTools.min.js
Added  /trunk/madman/Rpacks/seqplots/www/js/actionbutton.js
Added  /trunk/madman/Rpacks/seqplots/www/js/bootstrapSwitch.js
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Added  /trunk/madman/Rpacks/seqplots/www/js/d3.v3.min.js
Added  /trunk/madman/Rpacks/seqplots/www/js/dataTables.scroller.min.js
Added  /trunk/madman/Rpacks/seqplots/www/js/jquery.ba-throttle-debounce.js
Added  /trunk/madman/Rpacks/seqplots/www/js/jquery.dataTables.js
Added  /trunk/madman/Rpacks/seqplots/www/js/jquery.lettering.js
Added  /trunk/madman/Rpacks/seqplots/www/js/js_addons.js
Added  /trunk/madman/Rpacks/seqplots/www/js/load_finished.js
Added  /trunk/madman/Rpacks/seqplots/www/js/modal_events.js
Added  /trunk/madman/Rpacks/seqplots/www/js/nv.d3.min-new.js
Added  /trunk/madman/Rpacks/seqplots/www/js/tmpl.min.js
Added  /trunk/madman/Rpacks/seqplots/www/upload
Added  /trunk/madman/Rpacks/seqplots/www/upload/css
Added  /trunk/madman/Rpacks/seqplots/www/upload/css/jquery.fileupload-ui-noscript.css
Added  /trunk/madman/Rpacks/seqplots/www/upload/css/jquery.fileupload-ui.css
Added  /trunk/madman/Rpacks/seqplots/www/upload/css/style.css
Added  /trunk/madman/Rpacks/seqplots/www/upload/img
Added  /trunk/madman/Rpacks/seqplots/www/upload/img/loading.gif
Added  /trunk/madman/Rpacks/seqplots/www/upload/img/progressbar.gif
Added  /trunk/madman/Rpacks/seqplots/www/upload/js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/cors
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/cors/jquery.postmessage-transport.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/cors/jquery.xdr-transport.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/jquery.fileupload-fp.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/jquery.fileupload-ui.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/jquery.fileupload.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/jquery.iframe-transport.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/main.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/md5.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/vendor
Added  /trunk/madman/Rpacks/seqplots/www/upload/js/vendor/jquery.ui.widget.js
Added  /trunk/madman/Rpacks/seqplots/www/upload/upload.html
Start

From: przemol <pstempor@gmail.com>
Revision: 113469
Author: hpages
Date: 2016-02-10T00:10:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/NAMESPACE
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringSet-comparison.R
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringSet-comparison.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-comparison.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GenomicRanges-comparison.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/inter-range-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/R/List-comparison.R
Modified  /trunk/madman/Rpacks/IRanges/R/Ranges-comparison.R
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_Ranges-comparison.R
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-comparison.Rd
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Modified  /trunk/madman/Rpacks/IRanges/src/Ranges_comparison.c
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/NAMESPACE
Modified  /trunk/madman/Rpacks/S4Vectors/R/Hits-comparison.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/Vector-comparison.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/int-utils.R
Modified  /trunk/madman/Rpacks/S4Vectors/man/Hits-comparison.Rd
Modified  /trunk/madman/Rpacks/S4Vectors/man/Vector-comparison.Rd
Modified  /trunk/madman/Rpacks/S4Vectors/src/R_init_S4Vectors.c
Modified  /trunk/madman/Rpacks/S4Vectors/src/S4Vectors.h
Modified  /trunk/madman/Rpacks/S4Vectors/src/int_utils.c
Modified  /trunk/madman/Rpacks/S4Vectors/src/sort_utils.c
Modified  /trunk/madman/Rpacks/SummarizedExperiment/DESCRIPTION
Modified  /trunk/madman/Rpacks/SummarizedExperiment/NAMESPACE
Modified  /trunk/madman/Rpacks/SummarizedExperiment/R/RangedSummarizedExperiment-class.R
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/unitTests/test_RangedSummarizedExperiment-class.R
Modified  /trunk/madman/Rpacks/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/NAMESPACE
Modified  /trunk/madman/Rpacks/XVector/R/XRawList-comparison.R
Modified  /trunk/madman/Rpacks/XVector/man/XRawList-comparison.Rd
Modified  /trunk/madman/Rpacks/XVector/src/R_init_XVector.c
Modified  /trunk/madman/Rpacks/XVector/src/XRawList_comparison.c
Modified  /trunk/madman/Rpacks/XVector/src/XVector.h
Rename compare() -> pcompare(). For backward compatibility the old name still
works but now is just an "alias" for pcompare() and is deprecated.
Revision: 113468
Author: t.yin
Date: 2016-02-09T23:16:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/sevenbridges/R/cwl-import.R
Modified  /trunk/madman/Rpacks/sevenbridges/README.md
Deleted  /trunk/madman/Rpacks/sevenbridges/inst/docker/Dockerfile
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/devel
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/release
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/release/Dockerfile
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/release/report
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/release/src
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/release/src/performDE.R
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/rnaseqgene/release/src/performDE.Rmd
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif/Dockerfile
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif/README.md
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif/report
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif/report/report.Rmd
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif/src
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/runif/src/runif.R
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/sevenbridges
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/sevenbridges/devel
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/sevenbridges/devel/Dockerfile
Added  /trunk/madman/Rpacks/sevenbridges/inst/docker/sevenbridges/release
Added  /trunk/madman/Rpacks/sevenbridges/vignettes/bioc-workflow.Rmd
Modified  /trunk/madman/Rpacks/sevenbridges/vignettes/docker.Rmd
Added  /trunk/madman/Rpacks/sevenbridges/vignettes/rstudio.Rmd
add more docker stuff
Revision: 113467
Author: p.stempor
Date: 2016-02-09T23:11:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
vbump

From: przemol <pstempor@gmail.com>
Revision: 113466
Author: m.jiang
Date: 2016-02-09T22:17:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/R/gating-functions.R
Modified  /trunk/madman/Rpacks/openCyto/man/flowClust2d.Rd
Update flowClust.2d doc for param target
Revision: 113465
Author: m.jiang
Date: 2016-02-09T22:15:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/DESCRIPTION
bump
Revision: 113464
Author: m.jiang
Date: 2016-02-09T22:15:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/R/gating-methods.R
fix the bug that occurs in the edge cases
Revision: 113462
Author: hpages
Date: 2016-02-09T21:07:25+00:00
Paths:
Added  /trunk/madman/Rpacks/OnDiskSummarizedExperiment/inst
Added  /trunk/madman/Rpacks/OnDiskSummarizedExperiment/inst/scripts
Added  /trunk/madman/Rpacks/OnDiskSummarizedExperiment/inst/scripts/compare_assay_data_containers.R
Start comparing various assay data containers. Still need to figure out a good
way to do this in a more or less systematic way.
Revision: 113461
Author: d.tenenbaum
Date: 2016-02-09T20:41:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
handle it when stangle just adds .R to output filename instead of removing
previous suffix.
Revision: 113459
Author: hpages
Date: 2016-02-09T18:44:38+00:00
Paths:
Added  /trunk/madman/Rpacks/GenomicAlignments/vignettes/GenomicAlignmentsIntroduction.Rnw
oops, forgot to 'svn add' new vignette before previous commit
Revision: 113458
Author: hpages
Date: 2016-02-09T18:42:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/vignettes/GenomicRangesIntroduction.Rnw
Move the "Genomic Alignments" section to its own vignette in the
GenomicAlignments package.
Revision: 113457
Author: hpages
Date: 2016-02-09T18:11:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/vignettes/GenomicRangesIntroduction.Rnw
add a quick mention of the GPos class in the vignette
Revision: 113456
Author: hpages
Date: 2016-02-09T18:01:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GRanges-class.Rd
add a few more links to \seealso section of GPos man page
Revision: 113452
Author: v.obenchain
Date: 2016-02-09T17:20:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
part of commit r113415:

- use xml2 instead of XML for parsing (httr >= 1.1.0 dependency change)
Revision: 113451
Author: v.obenchain
Date: 2016-02-09T17:17:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/UCSCTrackUpdateChecker.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeAnnotationHubResource.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEncodeDCC.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblFasta.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblTwoBit.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEpigenomeRoadmap.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeGencodeFasta.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeGenecodeGFF.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeGrasp2Db.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makePazar.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeUCSCChain.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/trackWithAuxiliaryTableToGRangesRecipe.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/webAccessFunctions.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_recipe.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_webAccessFunctions.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/man/AnnotationHubMetadata-class.Rd
Deleted  /trunk/madman/Rpacks/AnnotationHubData/man/ensemblFastaToFaFile.Rd
Added  /trunk/madman/Rpacks/AnnotationHubData/man/makeEnsemblFasta.Rd
Added  /trunk/madman/Rpacks/AnnotationHubData/man/makeGencodeFasta.Rd
Modified  /trunk/madman/Rpacks/AnnotationHubData/man/updateResources.Rd
work on recipes:

- clean up ChEA and Gencode
- don't export tracksToUpdate(); was broken and not used
- reorg man pages; combine Ensembl Fasta and TwoBit on single man page
Revision: 113449
Author: mtmorgan
Date: 2016-02-09T16:40:37+00:00
Paths:
Added  /trunk/madman/Rpacks/BasicSTARRseq
Added  /trunk/madman/Rpacks/BasicSTARRseq/DESCRIPTION
Added  /trunk/madman/Rpacks/BasicSTARRseq/NAMESPACE
Added  /trunk/madman/Rpacks/BasicSTARRseq/R
Added  /trunk/madman/Rpacks/BasicSTARRseq/R/AllClasses.r
Added  /trunk/madman/Rpacks/BasicSTARRseq/R/AllGenerics.r
Added  /trunk/madman/Rpacks/BasicSTARRseq/R/getPeaks.R
Added  /trunk/madman/Rpacks/BasicSTARRseq/R/methods-STARRseqData.r
Added  /trunk/madman/Rpacks/BasicSTARRseq/inst
Added  /trunk/madman/Rpacks/BasicSTARRseq/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/BasicSTARRseq/inst/extdata
Added  /trunk/madman/Rpacks/BasicSTARRseq/inst/extdata/smallInput.bam
Added  /trunk/madman/Rpacks/BasicSTARRseq/inst/extdata/smallSTARR.bam
Added  /trunk/madman/Rpacks/BasicSTARRseq/man
Added  /trunk/madman/Rpacks/BasicSTARRseq/man/STARRseqData-class.Rd
Added  /trunk/madman/Rpacks/BasicSTARRseq/man/getPeaks.Rd
Added  /trunk/madman/Rpacks/BasicSTARRseq/vignettes
Added  /trunk/madman/Rpacks/BasicSTARRseq/vignettes/BasicSTARRseq.rnw
Added  /trunk/madman/Rpacks/EWCE
Added  /trunk/madman/Rpacks/EWCE/DESCRIPTION
Added  /trunk/madman/Rpacks/EWCE/NAMESPACE
Added  /trunk/madman/Rpacks/EWCE/R
Added  /trunk/madman/Rpacks/EWCE/R/add.res.to.merging.list.R
Added  /trunk/madman/Rpacks/EWCE/R/bootstrap.enrichment.test.R
Added  /trunk/madman/Rpacks/EWCE/R/cell.list.dist.R
Added  /trunk/madman/Rpacks/EWCE/R/data.R
Added  /trunk/madman/Rpacks/EWCE/R/ewce.plot.R
Added  /trunk/madman/Rpacks/EWCE/R/ewce_expression_data.R
Added  /trunk/madman/Rpacks/EWCE/R/generate.bootstrap.plots.R
Added  /trunk/madman/Rpacks/EWCE/R/merged_ewce.R
Added  /trunk/madman/Rpacks/EWCE/R/prepare.genesize.control.network.R
Added  /trunk/madman/Rpacks/EWCE/R/read_celltype_data.R
Added  /trunk/madman/Rpacks/EWCE/R/subcell.list.dist.R
Added  /trunk/madman/Rpacks/EWCE/data
Added  /trunk/madman/Rpacks/EWCE/data/celltype_data.rda
Added  /trunk/madman/Rpacks/EWCE/data/datalist
Added  /trunk/madman/Rpacks/EWCE/data/example_genelist.rda
Added  /trunk/madman/Rpacks/EWCE/data/mouse_to_human_homologs.rda
Added  /trunk/madman/Rpacks/EWCE/data/tt_alzh.rda
Added  /trunk/madman/Rpacks/EWCE/data/tt_alzh_BA36.rda
Added  /trunk/madman/Rpacks/EWCE/data/tt_alzh_BA44.rda
Added  /trunk/madman/Rpacks/EWCE/inst
Added  /trunk/madman/Rpacks/EWCE/man
Added  /trunk/madman/Rpacks/EWCE/man/add.res.to.merging.list.Rd
Added  /trunk/madman/Rpacks/EWCE/man/bootstrap.enrichment.test.Rd
Added  /trunk/madman/Rpacks/EWCE/man/celltype_data.Rd
Added  /trunk/madman/Rpacks/EWCE/man/ewce.plot.Rd
Added  /trunk/madman/Rpacks/EWCE/man/ewce_expression_data.Rd
Added  /trunk/madman/Rpacks/EWCE/man/example_genelist.Rd
Added  /trunk/madman/Rpacks/EWCE/man/generate.bootstrap.plots.Rd
Added  /trunk/madman/Rpacks/EWCE/man/merged_ewce.Rd
Added  /trunk/madman/Rpacks/EWCE/man/mouse_to_human_homologs.Rd
Added  /trunk/madman/Rpacks/EWCE/man/read_celltype_data.Rd
Added  /trunk/madman/Rpacks/EWCE/man/tt_alzh.Rd
Added  /trunk/madman/Rpacks/EWCE/man/tt_alzh_BA36.Rd
Added  /trunk/madman/Rpacks/EWCE/man/tt_alzh_BA44.Rd
Added  /trunk/madman/Rpacks/EWCE/vignettes
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_.none..pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____astrocytes.ependymal_Epend.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____endothelial.mural_Vsmc.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Mgl1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Mgl2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Pvm1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____microglia_Pvm2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____oligodendrocytes_Oligo2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____oligodendrocytes_Oligo3.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____oligodendrocytes_Oligo6.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists_LOG____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_.none..pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____astrocytes.ependymal_Epend.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____endothelial.mural_Vsmc.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Mgl1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Mgl2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Pvm1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____microglia_Pvm2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____oligodendrocytes_Oligo2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____oligodendrocytes_Oligo3.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____oligodendrocytes_Oligo6.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/bootDists____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_.none..pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____astrocytes.ependymal_Epend.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____endothelial.mural_Vsmc.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Mgl1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Mgl2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Pvm1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____microglia_Pvm2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____oligodendrocytes_Oligo2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____oligodendrocytes_Oligo3.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____oligodendrocytes_Oligo6.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_noText____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_.none..pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Astro1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Astro2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Choroid.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____astrocytes.ependymal_Epend.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____endothelial.mural_Vsmc.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Mgl1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Mgl2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Pvm1.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____microglia_Pvm2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____oligodendrocytes_Oligo2.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____oligodendrocytes_Oligo3.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____oligodendrocytes_Oligo6.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/BootstrapPlots/qqplot_wtGSym____VignetteGraphs____pyramidal.CA1_CA1PyrInt.pdf
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE.Rmd
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE.bib
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE_cache
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE_cache/html
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE_cache/html/__packages
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE_cache/html/unnamed-chunk-14_4411e5f4113b952f3920425bdf252363.RData
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE_cache/html/unnamed-chunk-14_4411e5f4113b952f3920425bdf252363.rdb
Added  /trunk/madman/Rpacks/EWCE/vignettes/EWCE_cache/html/unnamed-chunk-14_4411e5f4113b952f3920425bdf252363.rdx
Added  /trunk/madman/Rpacks/EWCE/vignettes/nature.csl
Added  /trunk/madman/Rpacks/RGraph2js
Added  /trunk/madman/Rpacks/RGraph2js/COPYING
Added  /trunk/madman/Rpacks/RGraph2js/DESCRIPTION
Added  /trunk/madman/Rpacks/RGraph2js/NAMESPACE
Added  /trunk/madman/Rpacks/RGraph2js/NEWS
Added  /trunk/madman/Rpacks/RGraph2js/R
Added  /trunk/madman/Rpacks/RGraph2js/R/RGraph2js-package.R
Added  /trunk/madman/Rpacks/RGraph2js/R/dataformating.R
Added  /trunk/madman/Rpacks/RGraph2js/R/graph2js.R
Added  /trunk/madman/Rpacks/RGraph2js/R/htmltemplate.R
Added  /trunk/madman/Rpacks/RGraph2js/R/jstemplate.R
Added  /trunk/madman/Rpacks/RGraph2js/R/utils.R
Added  /trunk/madman/Rpacks/RGraph2js/inst
Added  /trunk/madman/Rpacks/RGraph2js/inst/extdata
Added  /trunk/madman/Rpacks/RGraph2js/inst/extdata/nohosts.dot
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Added  /trunk/madman/Rpacks/RGraph2js/inst/resources/graphRenderer.min.js
Added  /trunk/madman/Rpacks/RGraph2js/inst/resources/images.zip
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Added  /trunk/madman/Rpacks/RGraph2js/inst/unitTests/getDefaultToolParameters.R
Added  /trunk/madman/Rpacks/RGraph2js/inst/unitTests/test_getEdgesDataFrame.R
Added  /trunk/madman/Rpacks/RGraph2js/inst/unitTests/test_getNodesDataFrame.R
Added  /trunk/madman/Rpacks/RGraph2js/man
Added  /trunk/madman/Rpacks/RGraph2js/man/generateOptionsJSCode.Rd
Added  /trunk/madman/Rpacks/RGraph2js/man/getAdjMat.Rd
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Added  /trunk/madman/Rpacks/RGraph2js/man/getEdgesDataFrame.Rd
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Added  /trunk/madman/Rpacks/RGraph2js/man/getJSCode.Rd
Added  /trunk/madman/Rpacks/RGraph2js/man/getNodesDataFrame.Rd
Added  /trunk/madman/Rpacks/RGraph2js/man/getUUID.Rd
Added  /trunk/madman/Rpacks/RGraph2js/man/graph2js.Rd
Added  /trunk/madman/Rpacks/RGraph2js/man/graph2json.Rd
Added  /trunk/madman/Rpacks/RGraph2js/tests
Added  /trunk/madman/Rpacks/RGraph2js/tests/runTests.R
Added  /trunk/madman/Rpacks/RGraph2js/vignettes
Added  /trunk/madman/Rpacks/RGraph2js/vignettes/RGraph2js.Rnw
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Added  /trunk/madman/Rpacks/RGraph2js/vignettes/zoomout.png
Added  /trunk/madman/Rpacks/ROTS
Added  /trunk/madman/Rpacks/ROTS/ChangeLog
Added  /trunk/madman/Rpacks/ROTS/DESCRIPTION
Added  /trunk/madman/Rpacks/ROTS/NAMESPACE
Added  /trunk/madman/Rpacks/ROTS/R
Added  /trunk/madman/Rpacks/ROTS/R/ROTS.R
Added  /trunk/madman/Rpacks/ROTS/R/RcppExports.R
Added  /trunk/madman/Rpacks/ROTS/R/biggerN.R
Added  /trunk/madman/Rpacks/ROTS/R/bootstrapSamples.R
Added  /trunk/madman/Rpacks/ROTS/R/calculateFDR.R
Added  /trunk/madman/Rpacks/ROTS/R/calculateOverlaps1.R
Added  /trunk/madman/Rpacks/ROTS/R/calculateOverlaps2.R
Added  /trunk/madman/Rpacks/ROTS/R/calculateP.R
Added  /trunk/madman/Rpacks/ROTS/R/permutatedSamples.R
Added  /trunk/madman/Rpacks/ROTS/R/print.ROTS.R
Added  /trunk/madman/Rpacks/ROTS/R/summary.ROTS.R
Added  /trunk/madman/Rpacks/ROTS/R/testStatistic.R
Added  /trunk/madman/Rpacks/ROTS/data
Added  /trunk/madman/Rpacks/ROTS/data/affySpikeIn.RData
Added  /trunk/madman/Rpacks/ROTS/man
Added  /trunk/madman/Rpacks/ROTS/man/ROTS.Rd
Added  /trunk/madman/Rpacks/ROTS/man/affySpikeIn.Rd
Added  /trunk/madman/Rpacks/ROTS/man/summary.ROTS.Rd
Added  /trunk/madman/Rpacks/ROTS/src
Added  /trunk/madman/Rpacks/ROTS/src/NeedForSpeed1.cpp
Added  /trunk/madman/Rpacks/ROTS/src/NeedForSpeed2.cpp
Added  /trunk/madman/Rpacks/ROTS/src/RcppExports.cpp
Added  /trunk/madman/Rpacks/ROTS/src/pvalue.cpp
Added  /trunk/madman/Rpacks/ROTS/vignettes
Added  /trunk/madman/Rpacks/ROTS/vignettes/ROTS.Rnw
Modified  /trunk/madman/Rpacks/bioc_3.3.manifest
Adding RGraph2js, ROTS, BasicSTARRseq, EWCE
Revision: 113448
Author: mtmorgan
Date: 2016-02-09T16:23:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/R/tracker.R
remove Jim Java from reviewer team
Revision: 113447
Author: s.zimmerman
Date: 2016-02-09T16:14:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/pathVar/DESCRIPTION
Modified  /trunk/madman/Rpacks/pathVar/NEWS
Modified  /trunk/madman/Rpacks/pathVar/inst/CITATION
Modified  /trunk/madman/Rpacks/pathVar/man/pathVar-package.Rd
modify citation file to print correct version
Revision: 113446
Author: j.java
Date: 2016-02-09T16:08:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/R/simplify.R
Better interaction with gmailr; version bump.
Revision: 113445
Author: m.kosinski
Date: 2016-02-09T15:55:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/RTCGA/.Rbuildignore
Modified  /trunk/madman/Rpacks/RTCGA/DESCRIPTION
Modified  /trunk/madman/Rpacks/RTCGA/R/datasetsTCGA.R
Modified  /trunk/madman/Rpacks/RTCGA/README.md
Modified  /trunk/madman/Rpacks/RTCGA/man/datasetsTCGA.Rd
synchro with github repo
Revision: 113444
Author: l.gatto
Date: 2016-02-09T14:56:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRolocGUI/DESCRIPTION
Modified  /trunk/madman/Rpacks/pRolocGUI/NEWS
Modified  /trunk/madman/Rpacks/pRolocGUI/vignettes/pRolocGUI.Rmd
Merge branch 'master' into devel

* master: (622 commits)
  update refs in vignette
  new gh devel version
  regenerate pRolocVis man page
  updated news
  Typos in vignettes
  update vignette
  New figs for vignette
  Fixed typos
  fixing previous import warnings - see issue #61
  reformat DESCRIPTION
  :::.validpRolocVisMethod
  further remove legacy
  remove legacy code
  cleaning up imports and dependencies
  remove legacy vignette
  update news
  New doc for compare
  Updated docs and renamed compare to comapre_legacy
  Fixed bugs
  Fixed foi bug
  ...

From: Laurent <lg390@cam.ac.uk>
Revision: 113443
Author: v.kiselev
Date: 2016-02-09T12:12:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/SC3/DESCRIPTION
Modified  /trunk/madman/Rpacks/SC3/R/shiny.R
remove factors from output objects, all columns are now either numeric or character
Revision: 113442
Author: hpages
Date: 2016-02-09T10:45:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
2 minor tweaks to GPos example
Revision: 113441
Author: hpages
Date: 2016-02-09T10:32:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
minor rephrasing
Revision: 113440
Author: hpages
Date: 2016-02-09T10:24:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
tidy up comment
Revision: 113439
Author: hpages
Date: 2016-02-09T10:21:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
rename internal helper .merge_adjacent_ranges() -> .stitch_GenomicRanges()
Revision: 113438
Author: hpages
Date: 2016-02-09T08:53:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GRanges-class.Rd
minor rephrasing
Revision: 113437
Author: hpages
Date: 2016-02-09T08:40:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GRangesList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GRanges-class.Rd
More work on GPos objects:
- Add "as.data.frame" method. The method returns a data frame with a "pos"
  column instead of the "start", "end", and "width" columns one gets when
  'x' is a GRanges object.
- Modify "show" method to display pos(x) instead of ranges(x).
- Add Accessors, Coercion, Subsetting, Combining, and Splitting and Relisting
  sections to the man page.
Revision: 113436
Author: hpages
Date: 2016-02-09T06:28:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/man/SNPlocs-class.Rd
The "snpsBySeqname", "snpsByOverlaps", and "snpsById" methods for SNPlocs
objects now return a GPos instead of GRanges object.
Revision: 113435
Author: h.klein
Date: 2016-02-09T04:06:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/epigenomix/man/MixModel-class.Rd
Fixed documentation.
Revision: 113434
Author: hpages
Date: 2016-02-09T03:49:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
small addition to GPos man page
Revision: 113433
Author: hpages
Date: 2016-02-09T03:24:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
various improvements to GPos man page
Revision: 113432
Author: h.klein
Date: 2016-02-09T01:07:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/epigenomix/DESCRIPTION
Modified  /trunk/madman/Rpacks/epigenomix/NAMESPACE
Modified  /trunk/madman/Rpacks/epigenomix/R/methods-MixModel.R
Method summary() for class MixModelBayes returns credible intervals in addition to parameter estimations.
Revision: 113431
Author: hpages
Date: 2016-02-08T23:18:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/XString-class.R
Modified  /trunk/madman/Rpacks/Biostrings/man/XString-class.Rd
add "showAsCell" method for XString objects
Revision: 113430
Author: stvjc
Date: 2016-02-08T23:02:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/transChunk.R
adding the TransStore structures, not yet exported
Revision: 113429
Author: s.gogarten
Date: 2016-02-08T22:36:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqVarTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/SeqVarTools/R/regression.R
Modified  /trunk/madman/Rpacks/SeqVarTools/inst/unitTests/test_regression.R
undid restriction on regression in variants monomorphic by outcome
Revision: 113427
Author: hpages
Date: 2016-02-08T21:35:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/MIndex-class.R
Modified  /trunk/madman/Rpacks/Biostrings/man/MIndex-class.Rd
Remove the coercion method from MIndex to CompressedNormalIRangesList added
at commit 113364. The coercion methods defined in IRanges now take care of
turning an MIndex object (or any RangesList derivative in general) into a
NormalIRangesList object.
Revision: 113425
Author: hpages
Date: 2016-02-08T21:03:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/Ranges-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/RangesList-class.R
Modified  /trunk/madman/Rpacks/IRanges/man/IRangesList-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/RangesList-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/src/CompressedIRangesList_class.c
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Modified  /trunk/madman/Rpacks/IRanges/src/SimpleRangesList_class.c
- More tweaks to set of coercion methods to go from RangesList to
  NormalIRangesList.
- Add 'use.names' arg to isNormal method for RangesList objects.
Revision: 113424
Author: m.jiang
Date: 2016-02-08T20:00:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/QUALIFIER/DESCRIPTION
bump

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