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Revision: 97129
Author: v.obenchain
Date: 2014-11-26T00:49:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/src/cigar_utils.c
fix off by one error when processing 'S' in query_locs_to_ref_locs()
Revision: 97128
Author: s.arora
Date: 2014-11-25T23:29:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/R/recommendBiocViews.R
code update

correct logic for recommendBiocViews
Revision: 97127
Author: stvjc
Date: 2014-11-25T22:48:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
fixed up enumerateByFDR to include fdr
Revision: 97126
Author: hpages
Date: 2014-11-25T22:16:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Resync with latest improvements to
IRanges:::NCList_find_overlaps_by_group_and_combine().
Revision: 97125
Author: hpages
Date: 2014-11-25T22:12:17+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 optimization of NCList_find_overlaps_by_group_and_combine() by avoiding
copying the input data to temporary buffers.
Revision: 97124
Author: m.love
Date: 2014-11-25T21:00:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/NAMESPACE
Modified  /trunk/madman/Rpacks/DESeq2/R/AllClasses.R
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/R/methods.R
Modified  /trunk/madman/Rpacks/DESeq2/R/plots.R
Modified  /trunk/madman/Rpacks/DESeq2/R/results.R
Modified  /trunk/madman/Rpacks/DESeq2/R/rlogTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/R/varianceStabilizingTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/inst/unitTests/test_results.R
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeq.Rd
Added  /trunk/madman/Rpacks/DESeq2/man/DESeq2-package.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqResults.Rd
Added  /trunk/madman/Rpacks/DESeq2/man/DESeqTransform.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/coef.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/counts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/design.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/dispersionFunction.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/dispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateDispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateSizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normalizationFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotDispEsts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotMA.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotPCA.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/results.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/rlog.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/sizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/varianceStabilizingTransformation.Rd
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
adding BiocGenerics plotPCA import and fixing many man pages
Revision: 97123
Author: stvjc
Date: 2014-11-25T20:14:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/NAMESPACE
Added  /trunk/madman/Rpacks/gQTLstats/R/queryVCF.R
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
Modified  /trunk/madman/Rpacks/gQTLstats/vignettes/gQTLstats.Rmd
enumeration tools are in
Revision: 97120
Author: m.carlson
Date: 2014-11-25T19:26:20+00:00
Paths:
Added  /trunk/madman/Rpacks/PROPER
Added  /trunk/madman/Rpacks/PROPER/DESCRIPTION
Added  /trunk/madman/Rpacks/PROPER/NAMESPACE
Added  /trunk/madman/Rpacks/PROPER/R
Added  /trunk/madman/Rpacks/PROPER/R/DEdetection.R
Added  /trunk/madman/Rpacks/PROPER/R/plots.R
Added  /trunk/madman/Rpacks/PROPER/R/power.R
Added  /trunk/madman/Rpacks/PROPER/R/simOptions.2grp.R
Added  /trunk/madman/Rpacks/PROPER/R/simOptions.util.R
Added  /trunk/madman/Rpacks/PROPER/R/simfuns.R
Added  /trunk/madman/Rpacks/PROPER/data
Added  /trunk/madman/Rpacks/PROPER/data/GE.human.RData
Added  /trunk/madman/Rpacks/PROPER/data/bottomly.RData
Added  /trunk/madman/Rpacks/PROPER/data/cheung.RData
Added  /trunk/madman/Rpacks/PROPER/data/datalist
Added  /trunk/madman/Rpacks/PROPER/data/gilad.RData
Added  /trunk/madman/Rpacks/PROPER/data/maqc.RData
Added  /trunk/madman/Rpacks/PROPER/data/pbmc.RData
Added  /trunk/madman/Rpacks/PROPER/doc
Added  /trunk/madman/Rpacks/PROPER/doc/NEWS
Added  /trunk/madman/Rpacks/PROPER/doc/PROPER.pdf
Added  /trunk/madman/Rpacks/PROPER/inst
Added  /trunk/madman/Rpacks/PROPER/inst/CITATION
Added  /trunk/madman/Rpacks/PROPER/man
Added  /trunk/madman/Rpacks/PROPER/man/RNAseq.SimOptions.2grp.Rd
Added  /trunk/madman/Rpacks/PROPER/man/comparePower.Rd
Added  /trunk/madman/Rpacks/PROPER/man/historicalData.Rd
Added  /trunk/madman/Rpacks/PROPER/man/plotPowerHist.Rd
Added  /trunk/madman/Rpacks/PROPER/man/plots.Rd
Added  /trunk/madman/Rpacks/PROPER/man/power.seqDepth.Rd
Added  /trunk/madman/Rpacks/PROPER/man/runSims.Rd
Added  /trunk/madman/Rpacks/PROPER/man/simRNAseq.Rd
Added  /trunk/madman/Rpacks/PROPER/man/summaryPower.Rd
Added  /trunk/madman/Rpacks/PROPER/vignettes
Added  /trunk/madman/Rpacks/PROPER/vignettes/FDC.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/PROPER.Rnw
Added  /trunk/madman/Rpacks/PROPER/vignettes/TD.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/all.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/filter.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/powers.pdf
Modified  /trunk/madman/Rpacks/bioc_3.1.manifest
Adds PROPER to the repos.
Revision: 97119
Author: n.servant
Date: 2014-11-25T18:30:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/HiTC/NEWS
change in setEnvDisplay to fix x11 bug. S. Thomas
Revision: 97118
Author: n.servant
Date: 2014-11-25T18:28:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/HiTC/DESCRIPTION
Modified  /trunk/madman/Rpacks/HiTC/R/mapC.R
change in setEnvDisplay to fix x11 bug. S. Thomas
Revision: 97117
Author: j.hill
Date: 2014-11-25T17:41:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/sangerseqR/inst/PolyPeakParser/polypeakfunctions.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c3db4732e690dcca1519bd895051659236e59117

    Fixed bug in Poly Peak Parser when reverse compliment reference sequence is provided.

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-25 10:41:11 -0700
Author date: 2014-11-25 10:41:11 -0700
Revision: 97114
Author: j.hill
Date: 2014-11-25T16:32:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/sangerseqR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 96d4a5b87a7868c4fc3df3995cd241f06a72c546

    Changed version number.

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-25 09:32:26 -0700
Author date: 2014-11-25 09:32:26 -0700
Revision: 97113
Author: j.hill
Date: 2014-11-25T16:24:40+00:00
Paths:
Added  /trunk/madman/Rpacks/sangerseqR/CITATION
Modified  /trunk/madman/Rpacks/sangerseqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/sangerseqR/NAMESPACE
Modified  /trunk/madman/Rpacks/sangerseqR/R/ReadFileFunctions.R
Modified  /trunk/madman/Rpacks/sangerseqR/R/sangerseqmethods.R
Modified  /trunk/madman/Rpacks/sangerseqR/man/PolyPeakParser.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/abif-class.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/chromatogram.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/makeBaseCalls.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/read.abif.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/read.scf.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/readsangerseq.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/sangerseq-class.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/sangerseqAccessors.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/scf-class.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/setAllelePhase.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 99194c06436383fc217f0ee501bb97b515f6703a

    Merge commit 'd531c69bec363581f286f314443ec57bac715038'

    Conflicts:
        DESCRIPTION

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-25 09:24:30 -0700
Author date: 2014-11-25 09:24:30 -0700

Commit id: 5697d751ea34eacff55d0919135c09b0155491f2

    Fixed errors with opening some .ab1 files.

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-24 15:44:13 -0700
Author date: 2014-11-24 15:44:13 -0700
Revision: 97112
Author: k.rue-albrecht
Date: 2014-11-25T16:01:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOexpress/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOexpress/NEWS
Modified  /trunk/madman/Rpacks/GOexpress/R/analysis.R
Modified  /trunk/madman/Rpacks/GOexpress/R/post_analysis.R
Modified  /trunk/madman/Rpacks/GOexpress/R/toolkit.R
Modified  /trunk/madman/Rpacks/GOexpress/data/microarray2dataset.RData
Modified  /trunk/madman/Rpacks/GOexpress/data/prefix2dataset.RData
Modified  /trunk/madman/Rpacks/GOexpress/man/GOexpress-package.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/expression_plot_symbol.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/expression_profiles_symbol.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/microarray2dataset.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/prefix2dataset.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 0b0e943a1a47f8570bfca484c9b7fea3bd229275

    Devel 1.1.3. Included methods to generate the prefix2dataset and microarray2dataset tables to make life easier when Ensembl Biomart is updated. Updated the tables themselves with latest Ensembl species and microarray additions. Also included some additional information in those tables, and updated the methods dealing with them.

Committed by: Kevin Rue
Author Name: Kevin Rue
Commit date: 2014-11-25 16:07:03 +0000
Author date: 2014-11-25 16:07:03 +0000
Revision: 97111
Author: h.fang
Date: 2014-11-25T15:34:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Modified  /trunk/madman/Rpacks/supraHex/NAMESPACE
Modified  /trunk/madman/Rpacks/supraHex/R/sBMH.r
Modified  /trunk/madman/Rpacks/supraHex/R/sCompReorder.r
Modified  /trunk/madman/Rpacks/supraHex/R/sPipeline.r
Modified  /trunk/madman/Rpacks/supraHex/R/sTrainBatch.r
Modified  /trunk/madman/Rpacks/supraHex/R/sTrainSeq.r
Modified  /trunk/madman/Rpacks/supraHex/inst/NEWS
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/CITATIONs.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/INSTALLATIONs.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/INSTALLATIONs_pre.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/README.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/demo/Hiratani.r
Added  /trunk/madman/Rpacks/supraHex/inst/staticdocs/demo/ISMB2014.r
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/demo/List_demos.txt
Modified  /trunk/madman/Rpacks/supraHex/man/sBMH.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sCompReorder.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDistance.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDmat.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDmatCluster.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDmatMinima.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sHexDist.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sHexGrid.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sInitial.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sMapOverlay.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sNeighAny.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sNeighDirect.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sPipeline.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTopology.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTrainBatch.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTrainSeq.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTrainology.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sWriteData.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visColoralpha.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visColorbar.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visColormap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visCompReorder.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visDmatCluster.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visDmatHeatmap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHeatmap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHeatmapAdv.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexComp.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexGrid.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexMapping.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexMulComp.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexPattern.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visKernels.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visTreeBootstrap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visVp.Rd
Bump to the version 1.5.1
Revision: 97110
Author: stvjc
Date: 2014-11-25T15:16:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLBase/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLBase/vignettes/gQTLBase.Rmd
minor tweaks for geuvStore usage
Revision: 97109
Author: j.leek
Date: 2014-11-25T15:14:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/sva/R/num.sv.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: bdd97589736c45b64abfdea1d0ed780bf72083fe

    Merge branch 'master' of https://github.com/jtleek/sva-devel

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:59 -0500
Author date: 2014-11-25 10:13:59 -0500

Commit id: 4b1d957d4744015ab40faa6fb7c49ee5ceb24fc7

    updated n.sv to do min(m,n) when using method=be

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:44 -0500
Author date: 2014-11-25 10:13:44 -0500
Revision: 97107
Author: a.oles
Date: 2014-11-25T13:31:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
version 4.9.4
- as.Image: coerce subclasses to 'Image'
Revision: 97106
Author: c.bartenhagen
Date: 2014-11-25T11:41:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/RSVSim/DESCRIPTION
Modified  /trunk/madman/Rpacks/RSVSim/R/Main.R
Modified  /trunk/madman/Rpacks/RSVSim/R/Misc.R
Modified  /trunk/madman/Rpacks/RSVSim/R/Simulation.R
Bugfixing: 1.Loading TDs from masked BSGenome hg19 package. 2.Repeat bias weights messed up when user passes them via parameter
Revision: 97105
Author: smyth
Date: 2014-11-25T11:35:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/plotMDS.DGEList.R
plotMDS.DGEList now stores axislabel depending on distance method used.
Revision: 97104
Author: s.aibar
Date: 2014-11-25T11:32:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/FGNet/NEWS
Modified  /trunk/madman/Rpacks/FGNet/R/3_clustersDistance.R
Modified  /trunk/madman/Rpacks/FGNet/man/clustersDistance.Rd
3.1.8 Added argument 'clustMethod' to 'clustersDistance' and changed default clustering method to 'average'
Revision: 97103
Author: smyth
Date: 2014-11-25T11:28:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/NAMESPACE
Modified  /trunk/madman/Rpacks/limma/R/arrayWeights.R
Modified  /trunk/madman/Rpacks/limma/R/neqc.R
Modified  /trunk/madman/Rpacks/limma/R/plotMDS.R
Modified  /trunk/madman/Rpacks/limma/R/plots-ma.R
Modified  /trunk/madman/Rpacks/limma/R/venn.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/plotMDS.Rd
Modified  /trunk/madman/Rpacks/limma/man/plotma.Rd
Modified  /trunk/madman/Rpacks/limma/man/venn.Rd
25 Nov 2014: limma 3.23.2

- plotMDS() now stores 'axislabel', depending on the method used to
  compute distances, and using this for axis labels.

- vennDiagram now fills circles with specified colors.

- voomWithQualityWeights() now stores observation weights and array
  weights separately.

- plotMA method for EListRaw objects.

- nec() and neqc() now remove the Eb component if it exists in an
  EListRaw object.
Revision: 97101
Author: hpages
Date: 2014-11-25T10:46:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/kebabs/DESCRIPTION
Modified  /trunk/madman/Rpacks/kebabs/src/ByteStringVector.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97100
Author: hpages
Date: 2014-11-25T10:37:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/src/alphabet.c
Modified  /trunk/madman/Rpacks/ShortRead/src/io.c
Modified  /trunk/madman/Rpacks/ShortRead/src/sampler.c
Modified  /trunk/madman/Rpacks/ShortRead/src/trim.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97099
Author: hpages
Date: 2014-11-25T10:29:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Modified  /trunk/madman/Rpacks/rtracklayer/src/twoBit.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97098
Author: hpages
Date: 2014-11-25T10:22:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/rSFFreader/DESCRIPTION
Modified  /trunk/madman/Rpacks/rSFFreader/src/SFF-io.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97097
Author: hpages
Date: 2014-11-25T10:16:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/src/fafile.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/utilities.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97096
Author: hpages
Date: 2014-11-25T09:58:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
Modify findOverlaps_GNCList() to take advantage of support for "on-the-fly
preprocessing" in IRanges:::NCList_find_overlaps_by_group_and_combine().
This speeds up and reduce memory usage of findOverlaps() on GRanges objects
when algorithm="nclist" even more.
Revision: 97095
Author: hpages
Date: 2014-11-25T09:51:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
NCList_find_overlaps_by_group_and_combine() now supports "on-the-fly
preprocessing". This will speedup and reduce memory usage of findOverlaps() on
GRanges objects when algorithm="nclist".
Revision: 97094
Author: v.petyuk
Date: 2014-11-25T07:57:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnID/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 5688e2f39db6aa0abc6ae5edb9fc59f427fb3fbe

    Merge branch 'master' of https://github.com/vladpetyuk/MSnID

Committed by: Vlad Petyuk
Author Name: Vlad Petyuk
Commit date: 2014-11-24 23:56:59 -0800
Author date: 2014-11-24 23:56:59 -0800

Commit id: 8a184ffbf9c7bba06432824bd3cddf7bf78e907e

    Merge branch 'master' of https://github.com/vladpetyuk/MSnID

Committed by: Vlad Petyuk
Author Name: Vlad Petyuk
Commit date: 2014-11-24 23:56:49 -0800
Author date: 2014-11-24 23:51:55 -0800
Revision: 97092
Author: v.petyuk
Date: 2014-11-25T07:52:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnID/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnID/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: bc7065c1f5adb5cd5bb02480ec636878f16aa78d

    Merge branch 'master' of https://github.com/vladpetyuk/MSnID

Committed by: Vlad Petyuk
Author Name: Vlad Petyuk
Commit date: 2014-11-24 23:51:55 -0800
Author date: 2014-11-24 23:51:55 -0800

Commit id: f77e6fee36805b14cc41a81a678c9bbd13e0c548

    update to accomodate multiple arguments in "id_quality" and "evaluate_filter" methods. Now the "level" argument is not limited to just one value. By default it is all three.

Committed by: Vlad Petyuk
Author Name: Vlad Petyuk
Commit date: 2014-11-24 23:51:36 -0800
Author date: 2014-11-24 23:44:56 -0800
Revision: 97091
Author: v.petyuk
Date: 2014-11-25T07:45:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnID/R/MSnID-methods.R
Modified  /trunk/madman/Rpacks/MSnID/R/optimize_filter.r
Modified  /trunk/madman/Rpacks/MSnID/inst/unitTests/test_apply_filter.R
Modified  /trunk/madman/Rpacks/MSnID/man/evaluate_filter.Rd
Modified  /trunk/madman/Rpacks/MSnID/man/id_quality.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e18cce4e42bac13596436d913792e9bf06f9621d

    update to accomodate multiple arguments in "id_quality" and "evaluate_filter" methods. Now the "level" argument is not limited to just one value. By default it is all three.

Committed by: Vlad Petyuk
Author Name: Vlad Petyuk
Commit date: 2014-11-24 23:44:56 -0800
Author date: 2014-11-24 23:44:56 -0800
Revision: 97090
Author: smyth
Date: 2014-11-25T07:08:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/NAMESPACE
Modified  /trunk/madman/Rpacks/edgeR/R/plotMDS.DGEList.R
Fix bug (introduced 20 Nov) to plotMDS.DGEList
Revision: 97088
Author: d.strbenac
Date: 2014-11-25T04:00:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
levels reordering in selectionPlot function corrected.
Revision: 97087
Author: m.love
Date: 2014-11-25T02:58:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/R/plots.R
Modified  /trunk/madman/Rpacks/DESeq2/R/rlogTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/man/rlog.Rd
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
adding proper match.arg for DESeq() test
Revision: 97086
Author: x.zheng
Date: 2014-11-25T01:06:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPRelate/NEWS
Modified  /trunk/madman/Rpacks/SNPRelate/R/AllUtilities.R
Modified  /trunk/madman/Rpacks/SNPRelate/R/Conversion.R
Modified  /trunk/madman/Rpacks/SNPRelate/man/snpgdsGDS2BED.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 500f7d5035d7fff23e672ef38165e98d66378b2e

    Update 'snpgdsTranspose'

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-11-24 17:06:13 -0800
Author date: 2014-11-24 17:06:13 -0800
Revision: 97085
Author: m.carlson
Date: 2014-11-25T01:05:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
comments and psuedocode that explores how we will deal with checking if we have a resource (or not).
Revision: 97084
Author: m.jiang
Date: 2014-11-24T23:55:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/src/GatingHierarchy.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/include/GatingHierarchy.hpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/macFlowJoWorkspace.cpp
Commit made by the Bioconductor Git-SVN bridge.
Consists of 8 commits.

Commit information:

Commit id: 0f47bbf3ecbcda2a9a657ac1af28ad8f5324e5b8

    Merge branch 'master' of github.com:RGLab/flowWorkspace

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-11-24 15:58:24 -0800
Author date: 2014-11-24 15:58:24 -0800

Commit id: 2b5cecc7468a1dd4c2ea99f6a9445eeb38dfbd5a

    Merge commit '22d4375bf98056dda03667b63ab11b57c14e1fc7'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-11-24 15:50:18 -0800
Author date: 2014-11-24 15:50:18 -0800

Commit id: 541b708c5f90876b7d2d6bef0a7c87ba534c6ae0

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-11-24 15:41:57 -0800
Author date: 2014-11-24 15:41:57 -0800

Commit id: 42cbaadbf92b8294677c9708d8d75b29b44c9f3c

    prevent the self-referral boolean gate

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-11-24 15:41:37 -0800
Author date: 2014-11-24 15:41:37 -0800

Commit id: 9f02b6e7581d697e60c252fb8f9819c7f6bfdd98

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-11-24 15:13:40 -0800
Author date: 2014-11-24 15:13:40 -0800

Commit id: 4d2aaf47313ed9f1314c96e89060fc62f6549877

    reslove cherry-pick conflicts

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-11-24 15:13:11 -0800
Author date: 2014-11-21 17:55:44 -0800

Commit id: 0467c6a0fa2d991fde43a33dde9917ed8b3b5c23

    change the way of searching reference node when parsing boolean gate

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-11-24 15:07:55 -0800
Author date: 2014-11-21 13:13:01 -0800

Commit id: 22d4375bf98056dda03667b63ab11b57c14e1fc7

    Creating branch for BioC 3.0 release.

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowWorkspace@95441 bc3139a8-67e5-0310-9ffc-ced21a209358

Committed by: d.tenenbaum
Author Name: d.tenenbaum
Commit date: 2014-10-13 21:46:02 +0000
Author date: 2014-10-13 21:46:02 +0000
Revision: 97082
Author: c.trapnell
Date: 2014-11-24T23:08:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/monocle/DESCRIPTION
Modified  /trunk/madman/Rpacks/monocle/R/methods-CellDataSet.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: abedf27fce25415760e4000bfd6eef6f9ca1ab1b

    reverted back to Tobit instead of cennorm

Committed by: ctrapnell
Author Name: ctrapnell
Commit date: 2014-11-24 11:43:11 -0800
Author date: 2014-11-24 11:43:11 -0800

Commit id: 97e43bd9bad4edfd43aa20ba390a29bd5af4ab28

    fixed an issue in the DESCRIPTION

Committed by: ctrapnell
Author Name: ctrapnell
Commit date: 2014-11-24 10:18:48 -0800
Author date: 2014-11-24 10:18:48 -0800
Revision: 97081
Author: m.carlson
Date: 2014-11-24T22:55:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.1.manifest
Added  /trunk/madman/Rpacks/cpvSNP
Added  /trunk/madman/Rpacks/cpvSNP/DESCRIPTION
Added  /trunk/madman/Rpacks/cpvSNP/NAMESPACE
Added  /trunk/madman/Rpacks/cpvSNP/NEWS
Added  /trunk/madman/Rpacks/cpvSNP/R
Added  /trunk/madman/Rpacks/cpvSNP/R/AllClasses.R
Added  /trunk/madman/Rpacks/cpvSNP/R/AllGenerics.R
Added  /trunk/madman/Rpacks/cpvSNP/R/GLOSSIResult-accessors.R
Added  /trunk/madman/Rpacks/cpvSNP/R/GeneSetResult-accessors.R
Added  /trunk/madman/Rpacks/cpvSNP/R/VEGASResult-accessors.R
Added  /trunk/madman/Rpacks/cpvSNP/R/assocPvalBySetPlot.R
Added  /trunk/madman/Rpacks/cpvSNP/R/createArrayData.R
Added  /trunk/madman/Rpacks/cpvSNP/R/geneToSNPList.R
Added  /trunk/madman/Rpacks/cpvSNP/R/glossi.R
Added  /trunk/madman/Rpacks/cpvSNP/R/glossiMarginal.R
Added  /trunk/madman/Rpacks/cpvSNP/R/plotPvals.R
Added  /trunk/madman/Rpacks/cpvSNP/R/show-methods.R
Added  /trunk/madman/Rpacks/cpvSNP/R/simulate_chisq.R
Added  /trunk/madman/Rpacks/cpvSNP/R/vegas.R
Added  /trunk/madman/Rpacks/cpvSNP/R/vegasMarginal.R
Added  /trunk/madman/Rpacks/cpvSNP/R/vegasPrep.R
Added  /trunk/madman/Rpacks/cpvSNP/data
Added  /trunk/madman/Rpacks/cpvSNP/data/datalist
Added  /trunk/madman/Rpacks/cpvSNP/data/geneSetAnalysis.RData
Added  /trunk/madman/Rpacks/cpvSNP/data/test_genesHg19.RData
Added  /trunk/madman/Rpacks/cpvSNP/data/test_snpsGSC.RData
Added  /trunk/madman/Rpacks/cpvSNP/inst
Added  /trunk/madman/Rpacks/cpvSNP/inst/unitTests
Added  /trunk/madman/Rpacks/cpvSNP/inst/unitTests/test_cpvSNP.R
Added  /trunk/madman/Rpacks/cpvSNP/man
Added  /trunk/madman/Rpacks/cpvSNP/man/GLOSSIResult-class.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/GLOSSIResultCollection-class.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/GeneSetResult-class.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/GeneSetResultCollection-class.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/VEGASResult-class.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/VEGASResultCollection-class.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/assocPvalBySetPlot.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/createArrayData.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/degreesOfFreedom-method.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/exampleArrayData.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/geneSetAnalysis.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/geneSetName-methods.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/geneSets.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/geneToSNPList.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/glossi.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/glossiMarginal.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/pValue-method.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/plotPvals.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/show-methods.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/simulate_chisq.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/simulatedStats-method.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/statistic-methods.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/vegas.Rd
Added  /trunk/madman/Rpacks/cpvSNP/man/vegasMarginal.Rd
Added  /trunk/madman/Rpacks/cpvSNP/tests
Added  /trunk/madman/Rpacks/cpvSNP/tests/runTests.R
Added  /trunk/madman/Rpacks/cpvSNP/vignettes
Added  /trunk/madman/Rpacks/cpvSNP/vignettes/cpvSNP.Rnw
Added  /trunk/madman/Rpacks/nethet
Added  /trunk/madman/Rpacks/nethet/DESCRIPTION
Added  /trunk/madman/Rpacks/nethet/NAMESPACE
Added  /trunk/madman/Rpacks/nethet/R
Added  /trunk/madman/Rpacks/nethet/R/auxfunc.R
Added  /trunk/madman/Rpacks/nethet/R/cvglasso.R
Added  /trunk/madman/Rpacks/nethet/R/diffnet.R
Added  /trunk/madman/Rpacks/nethet/R/diffregr.R
Added  /trunk/madman/Rpacks/nethet/R/ggmgsa.R
Added  /trunk/madman/Rpacks/nethet/R/mixglasso.R
Added  /trunk/madman/Rpacks/nethet/R/nethet.R
Added  /trunk/madman/Rpacks/nethet/R/netplot.R
Added  /trunk/madman/Rpacks/nethet/R/netsim.R
Added  /trunk/madman/Rpacks/nethet/inst
Added  /trunk/madman/Rpacks/nethet/inst/NEWS
Added  /trunk/madman/Rpacks/nethet/man
Added  /trunk/madman/Rpacks/nethet/man/EXPStep.mix.Rd
Added  /trunk/madman/Rpacks/nethet/man/MStepGlasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/NetHet-package.Rd
Added  /trunk/madman/Rpacks/nethet/man/agg.pval.Rd
Added  /trunk/madman/Rpacks/nethet/man/agg.score.iriz.scale.Rd
Added  /trunk/madman/Rpacks/nethet/man/agg.score.iriz.shift.Rd
Added  /trunk/madman/Rpacks/nethet/man/aggpval.Rd
Added  /trunk/madman/Rpacks/nethet/man/aic.glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/beta.mat.Rd
Added  /trunk/madman/Rpacks/nethet/man/beta.mat.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/bic.glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/buildDotPlotDataFrame.Rd
Added  /trunk/madman/Rpacks/nethet/man/bwprun_mixglasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/cv.fold.Rd
Added  /trunk/madman/Rpacks/nethet/man/cv.glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/diffnet_multisplit.Rd
Added  /trunk/madman/Rpacks/nethet/man/diffnet_pval.Rd
Added  /trunk/madman/Rpacks/nethet/man/diffnet_singlesplit.Rd
Added  /trunk/madman/Rpacks/nethet/man/diffregr_multisplit.Rd
Added  /trunk/madman/Rpacks/nethet/man/diffregr_pval.Rd
Added  /trunk/madman/Rpacks/nethet/man/diffregr_singlesplit.Rd
Added  /trunk/madman/Rpacks/nethet/man/dot_plot.Rd
Added  /trunk/madman/Rpacks/nethet/man/error.bars.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.my.ev2.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.my.ev2.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.my.ev3.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.my.ev3.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.ww.mat.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.ww.mat2.Rd
Added  /trunk/madman/Rpacks/nethet/man/est2.ww.mat2.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/export_network.Rd
Added  /trunk/madman/Rpacks/nethet/man/func.uinit.Rd
Added  /trunk/madman/Rpacks/nethet/man/generate_2networks.Rd
Added  /trunk/madman/Rpacks/nethet/man/generate_inv_cov.Rd
Added  /trunk/madman/Rpacks/nethet/man/getinvcov.Rd
Added  /trunk/madman/Rpacks/nethet/man/ggmgsa_multisplit.Rd
Added  /trunk/madman/Rpacks/nethet/man/ggmgsa_singlesplit.Rd
Added  /trunk/madman/Rpacks/nethet/man/glasso.invcor.Rd
Added  /trunk/madman/Rpacks/nethet/man/glasso.invcov.Rd
Added  /trunk/madman/Rpacks/nethet/man/glasso.parcor.Rd
Added  /trunk/madman/Rpacks/nethet/man/gsea.highdimT2.Rd
Added  /trunk/madman/Rpacks/nethet/man/gsea.iriz.Rd
Added  /trunk/madman/Rpacks/nethet/man/gsea.iriz.scale.Rd
Added  /trunk/madman/Rpacks/nethet/man/gsea.iriz.shift.Rd
Added  /trunk/madman/Rpacks/nethet/man/gsea.t2cov.Rd
Added  /trunk/madman/Rpacks/nethet/man/het_cv_glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/hugepath.Rd
Added  /trunk/madman/Rpacks/nethet/man/inf.mat.Rd
Added  /trunk/madman/Rpacks/nethet/man/invcov2parcor.Rd
Added  /trunk/madman/Rpacks/nethet/man/invcov2parcor_array.Rd
Added  /trunk/madman/Rpacks/nethet/man/lambda.max.Rd
Added  /trunk/madman/Rpacks/nethet/man/lambdagrid_lin.Rd
Added  /trunk/madman/Rpacks/nethet/man/lambdagrid_mult.Rd
Added  /trunk/madman/Rpacks/nethet/man/loglik_mix.Rd
Added  /trunk/madman/Rpacks/nethet/man/logratio.Rd
Added  /trunk/madman/Rpacks/nethet/man/logratio.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/make_grid.Rd
Added  /trunk/madman/Rpacks/nethet/man/mcov.Rd
Added  /trunk/madman/Rpacks/nethet/man/mixglasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/mixglasso_init.Rd
Added  /trunk/madman/Rpacks/nethet/man/mixglasso_ncomp_fixed.Rd
Added  /trunk/madman/Rpacks/nethet/man/mle.ggm.Rd
Added  /trunk/madman/Rpacks/nethet/man/my.ev2.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/my.p.adjust.Rd
Added  /trunk/madman/Rpacks/nethet/man/my.ttest.Rd
Added  /trunk/madman/Rpacks/nethet/man/my.ttest2.Rd
Added  /trunk/madman/Rpacks/nethet/man/mytrunc.method.Rd
Added  /trunk/madman/Rpacks/nethet/man/perm.diffregr_pval.Rd
Added  /trunk/madman/Rpacks/nethet/man/perm.diffregr_teststat.Rd
Added  /trunk/madman/Rpacks/nethet/man/plot.diffnet.Rd
Added  /trunk/madman/Rpacks/nethet/man/plot.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/plot.ggmgsa.Rd
Added  /trunk/madman/Rpacks/nethet/man/plot.nethetclustering.Rd
Added  /trunk/madman/Rpacks/nethet/man/plotCV.Rd
Added  /trunk/madman/Rpacks/nethet/man/plot_2networks.Rd
Added  /trunk/madman/Rpacks/nethet/man/print.nethetsummary.Rd
Added  /trunk/madman/Rpacks/nethet/man/q.matrix.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/q.matrix.diffregr3.Rd
Added  /trunk/madman/Rpacks/nethet/man/q.matrix.diffregr4.Rd
Added  /trunk/madman/Rpacks/nethet/man/q.matrix3.Rd
Added  /trunk/madman/Rpacks/nethet/man/q.matrix4.Rd
Added  /trunk/madman/Rpacks/nethet/man/scatter_plot.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_aic.glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_bic.glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_cv.glasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_cv1se.lasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_cvfix.lasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_cvmin.lasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_cvsqrt.lasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_cvtrunc.lasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_full.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_lasso.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_mb.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_mb2.Rd
Added  /trunk/madman/Rpacks/nethet/man/screen_shrink.Rd
Added  /trunk/madman/Rpacks/nethet/man/shapiro_screen.Rd
Added  /trunk/madman/Rpacks/nethet/man/sim_mix.Rd
Added  /trunk/madman/Rpacks/nethet/man/sim_mix_networks.Rd
Added  /trunk/madman/Rpacks/nethet/man/sparse_conc.Rd
Added  /trunk/madman/Rpacks/nethet/man/summary.diffnet.Rd
Added  /trunk/madman/Rpacks/nethet/man/summary.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/summary.ggmgsa.Rd
Added  /trunk/madman/Rpacks/nethet/man/summary.nethetclustering.Rd
Added  /trunk/madman/Rpacks/nethet/man/sumoffdiag.Rd
Added  /trunk/madman/Rpacks/nethet/man/symmkldist.Rd
Added  /trunk/madman/Rpacks/nethet/man/t2cov.lr.Rd
Added  /trunk/madman/Rpacks/nethet/man/t2diagcov.lr.Rd
Added  /trunk/madman/Rpacks/nethet/man/test.sd.Rd
Added  /trunk/madman/Rpacks/nethet/man/test.t2.Rd
Added  /trunk/madman/Rpacks/nethet/man/tr.Rd
Added  /trunk/madman/Rpacks/nethet/man/twosample_single_regr.Rd
Added  /trunk/madman/Rpacks/nethet/man/w.kldist.Rd
Added  /trunk/madman/Rpacks/nethet/man/ww.mat.Rd
Added  /trunk/madman/Rpacks/nethet/man/ww.mat.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/man/ww.mat2.Rd
Added  /trunk/madman/Rpacks/nethet/man/ww.mat2.diffregr.Rd
Added  /trunk/madman/Rpacks/nethet/src
Added  /trunk/madman/Rpacks/nethet/src/betamat_diffnet.c
Added  /trunk/madman/Rpacks/nethet/tests
Added  /trunk/madman/Rpacks/nethet/tests/testthat
Added  /trunk/madman/Rpacks/nethet/tests/testthat/mixglasso_tests.r
Added  /trunk/madman/Rpacks/nethet/tests/testthat/netsim_test.r
Added  /trunk/madman/Rpacks/nethet/vignettes
Added  /trunk/madman/Rpacks/nethet/vignettes/nethet.Rnw
Added  /trunk/madman/Rpacks/nethet/vignettes/nethet.bib
Adds nethet/ cpvSNP/  to the repos.
Revision: 97079
Author: l.collado-torres
Date: 2014-11-24T21:41:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/inst/basicExploration/basicExploration.Rmd
Modified  /trunk/madman/Rpacks/regionReport/vignettes/realVignettes/regionReport.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 60aa92a3a0572d52085652d8430e860186dd1239

    Wider output for session_info()

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-24 16:38:54 -0500
Author date: 2014-11-24 16:38:54 -0500
Revision: 97077
Author: l.collado-torres
Date: 2014-11-24T21:38:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderPlot/vignettes/realVignettes/derfinderPlot.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f9ecc9a85217d65d6071fb95cb654427ee962313

    Wider output for session_info()

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-24 16:37:29 -0500
Author date: 2014-11-24 16:37:29 -0500
Revision: 97074
Author: l.collado-torres
Date: 2014-11-24T21:36:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/R/mergeResults.R
Modified  /trunk/madman/Rpacks/derfinder/vignettes/realVignettes/derfinder.Rmd
Modified  /trunk/madman/Rpacks/derfinder/vignettes/realVignettes/derfinderAdvanced.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 8c4884eba984c3620673618b5a457bec6f4c950e

    Wider output for session_info()

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-24 16:36:08 -0500
Author date: 2014-11-24 16:36:08 -0500
Revision: 97073
Author: l.collado-torres
Date: 2014-11-24T21:35:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderHelper/vignettes/realVignettes/derfinderHelper.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f928bbce5b593ed96f4691537fd5623c73ea2b41

    Wider output for session_info()

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-24 16:35:49 -0500
Author date: 2014-11-24 16:35:49 -0500
Revision: 97072
Author: p.haverty
Date: 2014-11-24T20:40:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/R/bounds.R
Modified  /trunk/madman/Rpacks/genoset/R/rangeSummaries.R
Version: 1.21.0. added PACKAGE=genoset to all .Call that did not already have this
Revision: 97071
Author: j.gadin
Date: 2014-11-24T18:57:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllelicImbalance-package.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/mapbias-methods.R
Added  /trunk/madman/Rpacks/AllelicImbalance/man/makeMaskedFasta.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/refAllele.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 5bbb47d7ceea8719b7a57da6659ddf73dbdf5677

    impr fa-gen

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-11-24 19:45:05 +0100
Author date: 2014-11-24 19:45:05 +0100

Commit id: 2cc1275524c58493c8c67ac1a191ae53a2623d99

    bugfix ASEsetFromBam

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-11-24 18:46:16 +0100
Author date: 2014-11-24 18:46:16 +0100
Revision: 97069
Author: l.goldstein
Date: 2014-11-24T17:40:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/NAMESPACE
Modified  /trunk/madman/Rpacks/SGSeq/R/counts.R
Modified  /trunk/madman/Rpacks/SGSeq/R/main.R
Modified  /trunk/madman/Rpacks/SGSeq/man/analyzeFeatures.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/getBamInfo.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/getSGFeatureCounts.Rd
Added  /trunk/madman/Rpacks/SGSeq/man/makeSGFeatureCounts.Rd
Modified  /trunk/madman/Rpacks/SGSeq/man/predictTxFeatures.Rd
added argument counts_only for function getSGFeatureCounts; export makeSGFeatureCounts; allow sample_info to be a data.frame or DataFrame
Revision: 97068
Author: m.jiang
Date: 2014-11-24T16:07:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 97066
Author: hpages
Date: 2014-11-24T10:25:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
Minor findOverlaps_GNCList() speedup by using new
IRanges:::NCList_find_overlaps_by_group_and_combine() helper instead of
IRanges:::NCLists_find_overlaps_and_combine(). There is a last round of
improvements to come to this new helper that should make findOverlaps() on
GRanges objects 10x faster or more when using algorithm="nclist" than when
using algorithm="intervaltree". Memory usage will also be drastically reduced.
Revision: 97065
Author: hpages
Date: 2014-11-24T10:10:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
tidy code a little
Revision: 97064
Author: r.castelo
Date: 2014-11-24T10:04:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/annotationEngine.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/autosomalRecessiveHomozygous.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/methods-VariantFilteringParam.R
Added support for different genome sequences via BS genome packages.
Revision: 97063
Author: hpages
Date: 2014-11-24T10:01:58+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
Replace internal helper NCLists_find_overlaps_and_combine() with
NCList_find_overlaps_by_group_and_combine().
GenomicRanges:::findOverlaps_GNCList() will be modified to use the new helper.
Revision: 97062
Author: d.strbenac
Date: 2014-11-24T06:00:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/errorMap.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/man/errorMap.Rd
selectionPlot now keeps axis labels in same order when boxplots are rotated 90 degrees. errorMap has new axis labelling options.
Revision: 97058
Author: hpages
Date: 2014-11-24T00:27:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/src/XStringSet_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/XStringSet_io.c
Modified  /trunk/madman/Rpacks/Biostrings/src/XString_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/align_needwunsQS.c
Modified  /trunk/madman/Rpacks/Biostrings/src/align_pairwiseAlignment.c
Modified  /trunk/madman/Rpacks/Biostrings/src/align_utils.c
Modified  /trunk/madman/Rpacks/Biostrings/src/inject_code.c
Modified  /trunk/madman/Rpacks/Biostrings/src/letter_frequency.c
Modified  /trunk/madman/Rpacks/Biostrings/src/lowlevel_matching.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_PWM.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern_boyermoore.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern_indels.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern_shiftor.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict_ACtree2.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict_Twobit.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict_utils.c
Modified  /trunk/madman/Rpacks/Biostrings/src/replace_letter_at.c
Modified  /trunk/madman/Rpacks/Biostrings/src/translate.c
Modified  /trunk/madman/Rpacks/Biostrings/src/unstrsplit_methods.c
Modified  /trunk/madman/Rpacks/Biostrings/src/utils.c
Modified  /trunk/madman/Rpacks/Biostrings/src/xscat.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97057
Author: hpages
Date: 2014-11-24T00:05:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/src/XRawList_comparison.c
Modified  /trunk/madman/Rpacks/XVector/src/XVectorList_class.c
Modified  /trunk/madman/Rpacks/XVector/src/XVector_class.c
Modified  /trunk/madman/Rpacks/XVector/src/slice_methods.c
Modified  /trunk/madman/Rpacks/XVector/src/view_summarization_methods.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97051
Author: stvjc
Date: 2014-11-23T12:29:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLBase/DESCRIPTION
dealing with case again
Revision: 97050
Author: stvjc
Date: 2014-11-23T12:29:07+00:00
Paths:
Added  /trunk/madman/Rpacks/gQTLBase/vignettes/gQTLBase.Rmd
hope that this properly cased file goes in
Revision: 97049
Author: stvjc
Date: 2014-11-23T12:27:58+00:00
Paths:
Deleted  /trunk/madman/Rpacks/gQTLBase/vignettes/gqtlBase.Rmd
deal with case conflicts
Revision: 97048
Author: stvjc
Date: 2014-11-23T12:22:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLBase/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLBase/vignettes/gqtlBase.Rmd
various formatting issues addressed
Revision: 97047
Author: hpages
Date: 2014-11-23T08:46:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/inst/include/XVector_defines.h
Move Chars_holder, Ints_holder, and Doubles_holder typedefs to the S4Vectors
package.
Revision: 97046
Author: hpages
Date: 2014-11-23T08:45:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/inst/include/S4Vectors_defines.h
Move Chars_holder, Ints_holder, and Doubles_holder typedefs from the XVector
package.
Revision: 97045
Author: hpages
Date: 2014-11-23T06:06:24+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
small code simplification
Revision: 97043
Author: stvjc
Date: 2014-11-23T04:46:37+00:00
Paths:
Deleted  /trunk/madman/Rpacks/gQTLbase
removing obsolete wrong case instance
Revision: 97042
Author: bcarvalh
Date: 2014-11-23T04:45:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/pdInfoBuilder/DESCRIPTION
Modified  /trunk/madman/Rpacks/pdInfoBuilder/inst/pd.PKG.template/DESCRIPTION
Modified  /trunk/madman/Rpacks/pdInfoBuilder/inst/pd.PKG.template2/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 33b1aed700866cef1e2b3e97cc33f444b38f9a77

    Fixing dependency on RSQLite

Committed by: Benilton Carvalho
Author Name: Benilton Carvalho
Commit date: 2014-11-23 02:45:21 -0200
Author date: 2014-11-23 02:45:21 -0200
Revision: 97039
Author: bcarvalh
Date: 2014-11-23T04:30:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/pdInfoBuilder/DESCRIPTION
Modified  /trunk/madman/Rpacks/pdInfoBuilder/inst/pd.PKG.template/DESCRIPTION
Modified  /trunk/madman/Rpacks/pdInfoBuilder/inst/pd.PKG.template2/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6940d68f25287d4c6c0948ddbdc86795e8350b18

    Fixing version problems

Committed by: Benilton Carvalho
Author Name: Benilton Carvalho
Commit date: 2014-11-23 02:29:54 -0200
Author date: 2014-11-23 02:29:54 -0200
Revision: 97038
Author: khansen
Date: 2014-11-23T02:57:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/R/readPgf.R
Modified  /trunk/madman/Rpacks/affxparser/tests/readPgf.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 581bd4329fe1109fc8511a1634436c14c57315e4

    ROBUSTNESS: Make readPgf(..., indices=integer(0)) give an error until we know no dependencies assumes that it reads *all* the probesets.  When we know that, we'll open it up.

Committed by: hb
Author Name: hb
Commit date: 2014-11-22 18:55:55 -0800
Author date: 2014-11-22 18:55:55 -0800
Revision: 97037
Author: khansen
Date: 2014-11-23T02:33:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/DESCRIPTION
Modified  /trunk/madman/Rpacks/affxparser/Makefile
Modified  /trunk/madman/Rpacks/affxparser/R/readPgf.R
Modified  /trunk/madman/Rpacks/affxparser/src/R_affx_clf_pgf_parser.cpp
Modified  /trunk/madman/Rpacks/affxparser/tests/readPgf.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 9 commits.

Commit information:

Commit id: d55829083a0b9fb34bd0eb20f694b421422e545a

    CRLF -> LF

Committed by: Bengtsson
Author Name: Bengtsson
Commit date: 2014-11-22 18:23:13 -0800
Author date: 2014-11-22 18:23:13 -0800

Commit id: f12f055845148ea9c75c90f1052cf6689af4c4c6

    Bumped version

Committed by: Bengtsson
Author Name: Bengtsson
Commit date: 2014-11-22 18:19:39 -0800
Author date: 2014-11-22 18:19:39 -0800

Commit id: 2964ce6c619e0fa36ac9be4bcbe80404880c38c9

    Opening up for readPgf(..., indices=integer(0))

Committed by: Bengtsson
Author Name: Bengtsson
Commit date: 2014-11-22 18:08:40 -0800
Author date: 2014-11-22 18:08:40 -0800

Commit id: 85ce69b39cd663ba33e63ed142da91a1b6bb7883

    Added 'make build_fast' and 'make install_fast'

Committed by: hb
Author Name: hb
Commit date: 2014-11-22 17:46:11 -0800
Author date: 2014-11-22 17:46:11 -0800

Commit id: 67fc7e19c60bb6ef5cee56c61faf3611b5c2fe3e

    Dropped a debug message

Committed by: Bengtsson
Author Name: Bengtsson
Commit date: 2014-10-31 17:11:38 -0700
Author date: 2014-10-31 17:11:38 -0700

Commit id: afe379cb725baabd2f9dda42c89c7ec9481e636e

    BUG FIX: Rewrote how native code of readPgf() handles 'indices'.

Committed by: Bengtsson
Author Name: Bengtsson
Commit date: 2014-10-31 17:04:05 -0700
Author date: 2014-10-31 17:04:05 -0700

Commit id: 65f2c94336466cc724584883bf078cec1ac00a2a

    Merge branch 'devel' of github.com:HenrikBengtsson/affxparser into devel

    Conflicts:
        src/R_affx_clf_pgf_parser.cpp

Committed by: hb
Author Name: hb
Commit date: 2014-10-31 15:09:18 -0700
Author date: 2014-10-31 15:09:18 -0700

Commit id: cb61ecda8e3c669881733c09b5e14f61f0ee97a8

    Rewriting readPgf()

Committed by: hb
Author Name: hb
Commit date: 2014-10-31 15:02:49 -0700
Author date: 2014-10-31 15:02:49 -0700

Commit id: 33621d62cd1c362bdf3a5b610d2d3acddd80063e

    Trying to force error

Committed by: hb
Author Name: hb
Commit date: 2014-10-31 11:48:48 -0700
Author date: 2014-10-31 11:48:48 -0700
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
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Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixBinExample_d283d833c7660b5611f31dc8dc295ae9.rdx
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixExample_4d2dd76ea7beb664163adfba6cf426a3.RData
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixExample_4d2dd76ea7beb664163adfba6cf426a3.rdb
Added  /trunk/madman/Rpacks/genomation/vignettes/cache/graphics-ScoreMatrixExample_4d2dd76ea7beb664163adfba6cf426a3.rdx
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
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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
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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

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