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

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Revision: 127670
Author: r.cavalcante
Date: 2017-03-23T20:00:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Bump version to get Bioc to notice

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127669
Author: r.cavalcante
Date: 2017-03-23T19:57:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam_fast.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_nb.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_nb_fast.R
Bugfix: Minimum geneset size had incorrect check

* Turns out go_genes is a vector of Entrez IDs, not a binary vector.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127668
Author: r.cavalcante
Date: 2017-03-23T19:57:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam_fast.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_nb.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_nb_fast.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Tests ignore genesets with less than 15 genes

* Tests have difficulty converging when genesets have less than 15 genes.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127667
Author: s.white
Date: 2017-03-23T18:38:09+00:00
Paths:
Added  /trunk/madman/Rpacks/KEGGlincs/inst
Added  /trunk/madman/Rpacks/KEGGlincs/inst/CITATION
add inst directory and CITATION file

From: vandersm <vandersm@mail.uc.edu>
Revision: 127666
Author: m.riester
Date: 2017-03-23T18:06:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Fixed crash in gene-level p-value calculation.
Revision: 127665
Author: m.lawrence
Date: 2017-03-23T16:47:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/man/AlignedXStringSet-class.Rd
add link to rtracklayer example of using inverted()
Revision: 127664
Author: m.lawrence
Date: 2017-03-23T16:46:34+00:00
Paths:
Added  /trunk/madman/Rpacks/rtracklayer/inst/tests/test.xmfa
Modified  /trunk/madman/Rpacks/rtracklayer/man/XMFAFile-class.Rd
add a simple example of using XMFA data
Revision: 127663
Author: m.lawrence
Date: 2017-03-23T16:46:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Modified  /trunk/madman/Rpacks/rtracklayer/NAMESPACE
Modified  /trunk/madman/Rpacks/rtracklayer/R/chain.R
ensure that we get all the symbols we need
Revision: 127662
Author: m.lawrence
Date: 2017-03-23T16:44:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/R/xmfa.R
fix loading of inverted alignments from XMFA
Revision: 127661
Author: s.white
Date: 2017-03-23T16:05:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGlincs/README.md
update and fix images/links in README

From: vandersm <vandersm@mail.uc.edu>
Revision: 127660
Author: s.gassen
Date: 2017-03-23T15:47:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/FlowSOM/DESCRIPTION
Modified  /trunk/madman/Rpacks/FlowSOM/inst/NEWS
Modified  /trunk/madman/Rpacks/FlowSOM/man/AddFlowFrame.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/AggregateFlowFrames.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/BuildMST.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/BuildSOM.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/CountGroups.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/Dist.MST.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/FMeasure.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/FlowSOM.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/FlowSOMSubset.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/Initialize.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/MapDataToCodes.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/MetaClustering.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/NewData.Rd
Deleted  /trunk/madman/Rpacks/FlowSOM/man/PeaksAndValleys.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotCenters.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotClusters2D.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotGroups.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotMarker.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotNode.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotNumbers.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotPies.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotStars.Rd
Deleted  /trunk/madman/Rpacks/FlowSOM/man/PlotStarsSD.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/PlotVariable.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/ProcessGatingML.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/Purity.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/QueryStarPlot.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/ReadInput.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/SOM.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/SaveClustersToFCS.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/UpdateNodeSize.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/computeBackgroundColor.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/metaClustering_consensus.Rd
Modified  /trunk/madman/Rpacks/FlowSOM/man/plotStarLegend.Rd
Deleted  /trunk/madman/Rpacks/FlowSOM/src/FlowSOM.dll
Modified  /trunk/madman/Rpacks/FlowSOM/vignettes/FlowSOM.Rnw
Use seed in the vignette
Revision: 127659
Author: t.wang2
Date: 2017-03-23T15:04:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/anamiR/DESCRIPTION
Modified  /trunk/madman/Rpacks/anamiR/R/GSEA_ana.R
Modified  /trunk/madman/Rpacks/anamiR/R/GSEA_res.R
Modified  /trunk/madman/Rpacks/anamiR/R/differExp_discrete.R
GSEA_revised
Revision: 127658
Author: c.ruiz-arenas
Date: 2017-03-23T14:30:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/MEAL/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEAL/NAMESPACE
Modified  /trunk/madman/Rpacks/MEAL/R/0_AllClasses.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisRegionResults_Constructor.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisRegionResults_SettersGetters.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisRegionResults_plotRDA.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisRegionResults_plotRegionR2.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisRegionResults_show.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisResults_Constructor.R
Modified  /trunk/madman/Rpacks/MEAL/R/AnalysisResults_plotEWAS.R
Modified  /trunk/madman/Rpacks/MEAL/R/DAProbe.R
Modified  /trunk/madman/Rpacks/MEAL/R/DARegion.R
Modified  /trunk/madman/Rpacks/MEAL/R/DARegionAnalysis.R
Modified  /trunk/madman/Rpacks/MEAL/R/MEAL.R
Modified  /trunk/madman/Rpacks/MEAL/R/RDAset.R
Modified  /trunk/madman/Rpacks/MEAL/R/calculateRelevantSNPs.R
Modified  /trunk/madman/Rpacks/MEAL/R/computeRDAR2.R
Modified  /trunk/madman/Rpacks/MEAL/R/correlationMethExprs.R
Added  /trunk/madman/Rpacks/MEAL/R/correlationMethSNPs.R
Deleted  /trunk/madman/Rpacks/MEAL/R/multiCorrMethExprs.R
Modified  /trunk/madman/Rpacks/MEAL/man/AnalysisRegionResults-class.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/DAProbe.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/DARegion.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/DARegionAnalysis.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/MEAL.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/RDAset.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/computeRDAR2.Rd
Modified  /trunk/madman/Rpacks/MEAL/man/correlationMethExprs.Rd
Added  /trunk/madman/Rpacks/MEAL/man/correlationMethSNPs.Rd
Modified  /trunk/madman/Rpacks/MEAL/tests/testthat/test_04filters.R
Modified  /trunk/madman/Rpacks/MEAL/tests/testthat/test_08rangeAnalysis.R
Modified  /trunk/madman/Rpacks/MEAL/tests/testthat/test_11plotting.R
Modified  /trunk/madman/Rpacks/MEAL/tests/testthat/test_12RDA.R
Modified  /trunk/madman/Rpacks/MEAL/tests/testthat/test_13SNPsCalculation.R
Add new changes to devel
Bump version
Revision: 127657
Author: l.myint
Date: 2017-03-23T14:27:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/yamss/DESCRIPTION
Fix version and fix quote char

From: Leslie Myint <leslie.myint@gmail.com>
Revision: 127656
Author: l.myint
Date: 2017-03-23T14:27:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/yamss/inst/CITATION
Fix rebase

From: Leslie Myint <leslie.myint@gmail.com>
Revision: 127655
Author: b.gel
Date: 2017-03-23T13:58:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/karyoploteR/DESCRIPTION
Deleted  /trunk/madman/Rpacks/karyoploteR/R/plotChromosomeNames.R
Deleted  /trunk/madman/Rpacks/karyoploteR/R/plotCytobands.R
Deleted  /trunk/madman/Rpacks/karyoploteR/man/plotCytobands.Rd
Remove from svn plotCytobands. Bump version
Revision: 127654
Author: m.riester
Date: 2017-03-23T13:37:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Minor edits to vignette.
Revision: 127649
Author: p.angerer
Date: 2017-03-23T10:23:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/DESCRIPTION
Modified  /trunk/madman/Rpacks/destiny/R/aaa.r
fix superfluous window opening
Revision: 127648
Author: a.delabriere
Date: 2017-03-23T10:14:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/proFIA/DESCRIPTION
Modified  /trunk/madman/Rpacks/proFIA/NAMESPACE
Modified  /trunk/madman/Rpacks/proFIA/R/proFIA-package.R
Modified  /trunk/madman/Rpacks/proFIA/vignettes/proFIA-vignette.Rmd
Fixed the plot method import form ropls
Revision: 127647
Author: r.castelo
Date: 2017-03-23T08:05:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/vignettes/usingVariantFiltering.Rnw
Fixed text in vignette.

From: Robert Castelo <robert.castelo@upf.edu>
Revision: 127646
Author: r.castelo
Date: 2017-03-23T08:05:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/annotationEngine.R
Update the interface to query the new SNPlocs packages.

From: Robert Castelo <robert.castelo@upf.edu>
Revision: 127644
Author: x.zheng
Date: 2017-03-23T03:33:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/DESCRIPTION
Modified  /trunk/madman/Rpacks/gdsfmt/NEWS
Modified  /trunk/madman/Rpacks/gdsfmt/README.md
Modified  /trunk/madman/Rpacks/gdsfmt/inst/CITATION
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dStream.cpp
avoid deprecated values of LZ4 and update CITATION file
Revision: 127642
Author: j.barry
Date: 2017-03-23T01:56:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/imageHTS/CHANGES
Modified  /trunk/madman/Rpacks/imageHTS/DESCRIPTION
Modified  /trunk/madman/Rpacks/imageHTS/R/segmentation-segmentATH.R
storage mode fix in segmentATH function
Revision: 127641
Author: m.jiang
Date: 2017-03-22T23:47:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/R/AllClasses.R
Modified  /trunk/madman/Rpacks/flowWorkspace/man/booleanFilter-class.Rd
add examples for booleanFilter to illustrate how to handle special characters. #43
Revision: 127640
Author: m.djekidel
Date: 2017-03-22T23:42:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/R3CPET/DESCRIPTION
added the HiC biocViews tag

From: sirusb <djek.nad@gmail.com>
Revision: 127639
Author: m.riester
Date: 2017-03-22T22:47:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Added recommendation for smaller panels in vignette checklist.
Revision: 127638
Author: m.lawrence
Date: 2017-03-22T22:37:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/configure
Modified  /trunk/madman/Rpacks/rtracklayer/configure.ac
correct set PKG_CONFIG_PATH on the Mac
Revision: 127637
Author: m.jiang
Date: 2017-03-22T22:29:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggcyto/DESCRIPTION
Modified  /trunk/madman/Rpacks/ggcyto/NAMESPACE
Modified  /trunk/madman/Rpacks/ggcyto/R/geom_overlay.R
Modified  /trunk/madman/Rpacks/ggcyto/man/geom_overlay.Rd
add ncdfFlowList support for geom_overlay. #19
Revision: 127634
Author: m.riester
Date: 2017-03-22T21:33:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/NAMESPACE
Modified  /trunk/madman/Rpacks/PureCN/NEWS
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Fixed 1.5.55 check error; Fixed bug in chromosome plot; added chromosome plot to vignette.
Revision: 127632
Author: n.olson
Date: 2017-03-22T20:53:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeFeatures/vignettes/Example_16S_Annotation_Workflow.Rmd
fixed typo

From: nate-d-olson <nathandavidolson@gmail.com>
Revision: 127631
Author: n.olson
Date: 2017-03-22T20:53:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeFeatures/vignettes/Example_16S_Annotation_Workflow.Rmd
using accessor function

From: nate-d-olson <nathandavidolson@gmail.com>
Revision: 127630
Author: n.olson
Date: 2017-03-22T20:44:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeFeatures/.travis.yml
removed space

From: nate-d-olson <nathandavidolson@gmail.com>
Revision: 127629
Author: m.lawrence
Date: 2017-03-22T18:25:08+00:00
Paths:
Added  /trunk/madman/Rpacks/rtracklayer/INSTALL
add INSTALL file describing configuration of building against openssl
Revision: 127628
Author: l.zhu
Date: 2017-03-22T17:23:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
Added  /trunk/madman/Rpacks/GUIDEseq/inst/extdata/p5.index
Added  /trunk/madman/Rpacks/GUIDEseq/inst/extdata/p7.index
added p5.index and p7.index test files
Revision: 127627
Author: s.gogarten
Date: 2017-03-22T16:08:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GWASTools/NAMESPACE
Deleted  /trunk/madman/Rpacks/GWASTools/R/defunct.R
removed defunct functions
Revision: 127626
Author: j.romero
Date: 2017-03-22T16:06:14+00:00
Paths:
Deleted  /trunk/madman/Rpacks/EventPointer/DESCRIPTION.orig
Remove .orig

From: unknown <jpromero@PCDOCCOM464B.tecnun.es>
Revision: 127624
Author: a.lun
Date: 2017-03-22T15:53:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/csaw/R/consolidateSizes.R
Modified  /trunk/madman/Rpacks/csaw/R/detailRanges.R
Modified  /trunk/madman/Rpacks/csaw/R/getPESizes.R
Switched to pre-allocate and fill.
Revision: 127621
Author: v.obenchain
Date: 2017-03-22T15:33:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGREST/DESCRIPTION
Modified  /trunk/madman/Rpacks/KEGGREST/R/KEGGREST.R
Modified  /trunk/madman/Rpacks/KEGGREST/R/parsers.R
Modified  /trunk/madman/Rpacks/KEGGREST/inst/unitTests/test_KEGGREST.R
fix bug in keggList(); thanks to Alexey Sergushichev for the patch
Revision: 127620
Author: t.hardcastle
Date: 2017-03-22T15:10:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/baySeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/baySeq/R/densDensityFunctions.R
Modified  /trunk/madman/Rpacks/baySeq/R/densityFunctions.R
Modified  /trunk/madman/Rpacks/baySeq/R/getLikelihoods.R
Modified  /trunk/madman/Rpacks/baySeq/R/getPriors_Generic.R
Modified  /trunk/madman/Rpacks/baySeq/vignettes/baySeq_generic.tex
2.9.2 fix to allow factors in sampleObservables slot
Revision: 127618
Author: m.love
Date: 2017-03-22T14:34:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/tximport/DESCRIPTION
Modified  /trunk/madman/Rpacks/tximport/R/infReps.R
fixing sailfish aux dir bug
Revision: 127616
Author: j.romero
Date: 2017-03-22T14:14:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/EventPointer/DESCRIPTION
Added  /trunk/madman/Rpacks/EventPointer/DESCRIPTION.orig
Added  /trunk/madman/Rpacks/EventPointer/inst/CITATION
Deleted  /trunk/madman/Rpacks/EventPointer/inst/CITATION.R
Added  /trunk/madman/Rpacks/EventPointer/vignettes/Thumbs.db
Resolved merge conflicts

From: unknown <jpromero@PCDOCCOM464B.tecnun.es>
Revision: 127615
Author: g.klambauer
Date: 2017-03-22T12:51:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/cn.mops/DESCRIPTION
Modified  /trunk/madman/Rpacks/cn.mops/NAMESPACE
Modified  /trunk/madman/Rpacks/cn.mops/R/getReadCountsFromBAM.R
Modified  /trunk/madman/Rpacks/cn.mops/R/getSegmentReadCountsFromBAM.R
Modified  /trunk/madman/Rpacks/cn.mops/man/calcFractionalCopyNumbers-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/calcIntegerCopyNumbers-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/cn.mops.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/cnvr-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/cnvs-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/exomecn.mops.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/getReadCountsFromBAM.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/getSegmentReadCountsFromBAM.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/gr-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/haplocn.mops.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/individualCall-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/iniCall-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/integerCopyNumber-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/localAssessments-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/makeRobustCNVR.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/normalizeChromosomes.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/normalizeGenome.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/normalizedData-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/params-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/posteriorProbs-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/referencecn.mops.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/sampleNames-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/segment.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/segmentation-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/segplot-CNVDetectionResult-method.Rd
Modified  /trunk/madman/Rpacks/cn.mops/man/singlecn.mops.Rd
Modified  /trunk/madman/Rpacks/cn.mops/vignettes/cn.mops.Rnw
Updated the getReadCountsFunctions with exomecopy's variant
Revision: 127613
Author: a.oles
Date: 2017-03-22T12:37:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/normalize.R
Modified  /trunk/madman/Rpacks/EBImage/src/normalize.c
version 4.17.29
- avoid object duplication in 'normalize' C function

From: aoles <andrzej.oles@gmail.com>
Revision: 127612
Author: w.kopp
Date: 2017-03-22T11:19:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/motifcounter/DESCRIPTION
Modified  /trunk/madman/Rpacks/motifcounter/vignettes/motifcounter.Rmd
minor changes of vignette usage examples
Revision: 127608
Author: a.lun
Date: 2017-03-22T09:42:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/csaw/src/get_cluster_stats.cpp
Bug fix to avoid segfault.
Revision: 127607
Author: stvjc
Date: 2017-03-22T09:36:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GGtools/man/All.cis.Rd
Modified  /trunk/madman/Rpacks/GGtools/man/eqtlTests.Rd
Modified  /trunk/madman/Rpacks/GGtools/tests/cis.R
remove unix.time and stop cis test on windows where memory consumption is too large
Revision: 127606
Author: y.zheng
Date: 2017-03-22T09:10:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/REMP/DESCRIPTION
Modified  /trunk/madman/Rpacks/REMP/inst/NEWS
Modified  /trunk/madman/Rpacks/REMP/vignettes/REMP.Rnw
0.99.25

From: Yinan Zheng <y-zheng@northwestern.edu>
Revision: 127605
Author: l.zappia
Date: 2017-03-22T06:44:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/splatter/DESCRIPTION
Modified  /trunk/madman/Rpacks/splatter/NAMESPACE
Modified  /trunk/madman/Rpacks/splatter/NEWS.md
Modified  /trunk/madman/Rpacks/splatter/R/SCESet-functions.R
Modified  /trunk/madman/Rpacks/splatter/R/compare.R
Modified  /trunk/madman/Rpacks/splatter/R/lun2-estimate.R
Modified  /trunk/madman/Rpacks/splatter/R/splat-simulate.R
Modified  /trunk/madman/Rpacks/splatter/man/addFeatureStats.Rd
Modified  /trunk/madman/Rpacks/splatter/man/compareSCESets.Rd
Added  /trunk/madman/Rpacks/splatter/man/diffSCESets.Rd
Modified  /trunk/madman/Rpacks/splatter/tests/testthat/test-splat-simulate.R
Modified  /trunk/madman/Rpacks/splatter/vignettes/splatter.Rmd
Merge branch 'master' into devel

* master:
  Version 0.99.12
  Run checks
  Warn if bcv.df is infinite
  Update addFeatureStats col names
  Update progress message
  Switch to boxplots in compareSCESets
  Change Lun2 nGenes estimate
  Add diffSCESets to vignette
  Add diffSCESets function

From: Luke Zappia <lazappi@users.noreply.github.com>
Revision: 127604
Author: m.djekidel
Date: 2017-03-22T04:24:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/R3CPET/DESCRIPTION
Modified  /trunk/madman/Rpacks/R3CPET/R/ChromMaintainers-methods.r
Modified  /trunk/madman/Rpacks/R3CPET/inst/NEWS
Modified  /trunk/madman/Rpacks/R3CPET/man/InferNetworks-methods.Rd
Modified  /trunk/madman/Rpacks/R3CPET/vignettes/R3CPET.Rnw
updated version number and NEWs

From: sirusb <djek.nad@gmail.com>
Revision: 127603
Author: s.su
Date: 2017-03-22T02:58:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/Glimma/.travis.yml
Updated yaml file
Revision: 127602
Author: m.jiang
Date: 2017-03-21T23:04:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowStats/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowStats/NAMESPACE
fix some missing imports from fda
Revision: 127601
Author: a.kucukural
Date: 2017-03-21T22:17:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/debrowser/DESCRIPTION
Modified  /trunk/madman/Rpacks/debrowser/NAMESPACE
Modified  /trunk/madman/Rpacks/debrowser/R/QCSection.R
Added  /trunk/madman/Rpacks/debrowser/R/bookmark.R
Modified  /trunk/madman/Rpacks/debrowser/R/condSelect.R
Modified  /trunk/madman/Rpacks/debrowser/R/heatmap.R
Modified  /trunk/madman/Rpacks/debrowser/R/load_data.R
Modified  /trunk/madman/Rpacks/debrowser/R/pca.R
Modified  /trunk/madman/Rpacks/debrowser/R/prepdata.R
Modified  /trunk/madman/Rpacks/debrowser/R/server.R
Modified  /trunk/madman/Rpacks/debrowser/R/startShiny.R
Modified  /trunk/madman/Rpacks/debrowser/R/ui.R
Modified  /trunk/madman/Rpacks/debrowser/R/uifuncs.R
Modified  /trunk/madman/Rpacks/debrowser/README.md
Added  /trunk/madman/Rpacks/debrowser/man/bookmarkServer.Rd
Added  /trunk/madman/Rpacks/debrowser/man/bookmarkUI.Rd
Added  /trunk/madman/Rpacks/debrowser/man/copy2newDirectory.Rd
Added  /trunk/madman/Rpacks/debrowser/man/getConditionSelectorFromMeta.Rd
Added  /trunk/madman/Rpacks/debrowser/man/getJsonObj.Rd
Modified  /trunk/madman/Rpacks/debrowser/man/getSelHeat.Rd
Modified  /trunk/madman/Rpacks/debrowser/man/getSelectInputBox.Rd
Added  /trunk/madman/Rpacks/debrowser/man/get_state_id.Rd
Added  /trunk/madman/Rpacks/debrowser/man/removeBookmark.Rd
Modified  /trunk/madman/Rpacks/debrowser/svn-commit.tmp
Modified  /trunk/madman/Rpacks/debrowser/vignettes/DEBrowser.Rmd
bug fixes
Revision: 127598
Author: m.teng
Date: 2017-03-21T21:54:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/rnaseqcomp/DESCRIPTION
Modified  /trunk/madman/Rpacks/rnaseqcomp/vignettes/rnaseqcomp.bib
Modified  /trunk/madman/Rpacks/rnaseqcomp/vignettes/rnaseqcomp.pdf
update
Revision: 127597
Author: j.ou
Date: 2017-03-21T21:49:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/R/oligoSummary.R
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/inst/NEWS
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/vignettes/pipeline.Rmd
Fix the bug that unable to find an inherited method for function
    'reverseComplement' for signature '"BString"' in oligoSummary function.
Revision: 127596
Author: t.silva
Date: 2017-03-21T21:27:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/man/GDCquery.Rd
removing part that is not running in bioc server (winodws only)
Revision: 127595
Author: t.silva
Date: 2017-03-21T21:10:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/mutation.Rmd
removing part that is not running in bioc server (winodws only)
Revision: 127593
Author: b.mifsud
Date: 2017-03-21T18:10:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOTHiC/R/GOTHiC.R
fixed bug in fragment mapping in GOTHiChicup function
Revision: 127592
Author: r.cavalcante
Date: 2017-03-21T17:50:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Modified  /trunk/madman/Rpacks/chipenrich/R/setup.R
Modified  /trunk/madman/Rpacks/chipenrich/R/utils.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.Rmd
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_ldef_geneid.txt
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_ldef_noextras.txt
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_ldef_nosymbol.txt
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_ldef_symbol.txt
Added  /trunk/madman/Rpacks/chipenrich/man/setup_ldef.Rd
Added  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_custom_ldef.R
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Harmonize custom LocusDefinition with class changes

* In recent chipenrich.data updates (v1.11.1+) gene symbols are included in the data.frame and GRanges of LocusDefinitions by default as a 'symbol' column.
* Custom locus definitions need to have a 'symbol' column added, and so setup_ldef() has been modified to get eg2symbol mappings from a 'genome' or to use the 'symbol' column provided by the user.
* Added blurb to vignette.
* Added tests to make sure function works.
* Some NAMESPACE and DESCRIPTION changes to get rid of build warnings.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127591
Author: r.cavalcante
Date: 2017-03-21T17:50:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Forgot to import BIocGenerics

* Needed for specific call to unlist() in randomize_locusdef()

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127590
Author: r.cavalcante
Date: 2017-03-21T17:50:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Fix option reporting in chipenrich()

* Use sys.call() instead of as.list(environment()).
* The old way would print entire data.frames of peaks in some instances, whereas sys.call() will only report the options used in the chipenrich() call.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127589
Author: r.cavalcante
Date: 2017-03-21T17:50:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/randomize.R
Refactor randomize_locusdef()

* SO MUCH FASTER!

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127588
Author: r.cavalcante
Date: 2017-03-21T17:49:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/assign_peaks.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/peaks_per_gene.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Modified  /trunk/madman/Rpacks/chipenrich/R/randomize.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/R/setup.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_approx.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_binomial.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_fisher.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam_fast.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_nb.R
Modified  /trunk/madman/Rpacks/chipenrich/R/test_nb_fast.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.Rmd
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Modified  /trunk/madman/Rpacks/chipenrich/man/assign_peak_segments.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/assign_peaks.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/calc_peak_gene_overlap.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/chipenrich.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/num_peaks_per_gene.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_gene_coverage.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_spline_length.Rd
Added  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_2_assign_peaks.R
Added  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_3_peaks_per_gene.R
Deleted  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_assign_peaks.R
Deleted  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_peaks_per_gene.R
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Harmonize chipenrich with chipenrich.data v1.11.1

* All instances of columns named 'geneid' are now 'gene_id'. Mappability data objects have their columns renamed to use 'gene_id'. This is because so much of the Bioconductor infrastructure locks you into the usage of 'gene_id' and it would be easier to use the same thing everywhere.
* Add gene symbols to assign_peaks() and assign_peak_segments() instead of in chipenrich().
* Change name of ldef 10kb_and_more_upstream to 10kb_outside_upstream
* Updated vignette to describe new locus definitions
* Updated documentation
* Updated unit tests since new locus definitions changed some of the results.
* Builds will fail on Travis and Bioc until chipenrich.data v1.11.1 appears there.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127587
Author: r.cavalcante
Date: 2017-03-21T17:49:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Bugfix for organism + geneset checki in chipenrich()

* Incorrect check prevented runs for valid combinations, e.g. mm10 + GO.
* Not sure how this hasn't cropped up in all our runs, but thanks to jamie.gearing for pointing it out.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127586
Author: r.cavalcante
Date: 2017-03-21T17:49:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.Rmd
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_header.txt
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_noheader.txt
Modified  /trunk/madman/Rpacks/chipenrich/man/load_peaks.Rd
Added  /trunk/madman/Rpacks/chipenrich/man/postprocess_peak_grs.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/read_bed.Rd
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_1_peak_input.R
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Add back arbitrary extension support for peaks

* Add back arbitrary extension support to read_bed(), so long as first three columns are chr, start, end, and there is no header. Users should comment out the header row if there is one.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127585
Author: r.cavalcante
Date: 2017-03-21T17:49:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/assign_peaks.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.Rmd
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test.bedGraph
Modified  /trunk/madman/Rpacks/chipenrich/inst/extdata/test.gff3
Modified  /trunk/madman/Rpacks/chipenrich/inst/extdata/test.gff3.gz
Modified  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_header.bed
Modified  /trunk/madman/Rpacks/chipenrich/man/assign_peak_segments.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/assign_peaks.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/calc_peak_gene_overlap.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/chipenrich.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/load_peaks.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/num_peaks_per_gene.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_dist_to_tss.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_gene_coverage.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_spline_length.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/read_bed.Rd
Deleted  /trunk/madman/Rpacks/chipenrich/man/read_bedgff.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_genesets.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_genomes.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_locusdefs.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_methods.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_read_lengths.Rd
Added  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_1_peak_input.R
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_assign_peaks.R
Deleted  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_peak_input.R
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_peaks_per_gene.R
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Refactor peak importing functions

* Refactor read_bed() to use rtracklayer::import(). Now handles the following formats (compressed or not): BED3 - BED6, broadPeak, narrowPeak, gff3, gff2, gff, gtf, wig, or bedGraph. Needed for future methods that may use signalValue for weights. Function has a genome argument which defaults to NA, but inherits the genome from chipenrich().
* Refactor load_peaks() to use GenomicRanges::makeGRangesFromDataFrame() instead of custom implementation. Use the keep.extra.columns argument to enable use of extra columns for weights as well. Function has a genome argument which defaults to NA, but inherits the genome from chipenrich().
* No longer GenomicRanges::reduce() the peaks because then you lose the extra columns. Now a warning is thrown if regions are not disjoint.
* Corresponding documentation, example, and vignette changes.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127584
Author: r.cavalcante
Date: 2017-03-21T17:49:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Fix code for num_peaks

* Early in development, the result of read_bed() must have been a list of IRanges, but now it's GRanges. Old way took an unexpectedly long time.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 127583
Author: m.jiang
Date: 2017-03-21T17:32:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQ/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQ/R/qaProcessFunctions.R
 updates according to RGLab/flowCore#70
Revision: 127582
Author: j.romero
Date: 2017-03-21T17:06:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/EventPointer/DESCRIPTION
Modified  /trunk/madman/Rpacks/EventPointer/inst/CITATION.R
Fixed Citation

From: unknown <jpromero@PCDOCCOM464B.tecnun.es>
Revision: 127581
Author: j.romero
Date: 2017-03-21T16:51:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/EventPointer/DESCRIPTION
Added  /trunk/madman/Rpacks/EventPointer/inst/CITATION.R
Merge branch 'master' into devel

* master:
  Update to DESCRIPTION and added Citation

From: unknown <jpromero@PCDOCCOM464B.tecnun.es>
Revision: 127580
Author: j.romero
Date: 2017-03-21T16:51:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/EventPointer/DESCRIPTION
Deleted  /trunk/madman/Rpacks/EventPointer/inst/CITATION.R
Update

From: unknown <jpromero@PCDOCCOM464B.tecnun.es>
Revision: 127579
Author: j.romero
Date: 2017-03-21T16:50:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/EventPointer/DESCRIPTION
Added  /trunk/madman/Rpacks/EventPointer/inst/CITATION.R
Update to DESCRIPTION and Citation added

From: unknown <jpromero@PCDOCCOM464B.tecnun.es>
Revision: 127578
Author: l.zhu
Date: 2017-03-21T16:50:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/findgRNAs.R
fixed a bug in findgRNAs.R to have gRNA.pattern work properly
Revision: 127576
Author: a.kuhn
Date: 2017-03-21T16:44:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/annotationTools/inst/NEWS.Rd
Corrected NEWS file.
Revision: 127575
Author: l.collado-torres
Date: 2017-03-21T16:40:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/recount/DESCRIPTION
Modified  /trunk/madman/Rpacks/recount/NEWS
Modified  /trunk/madman/Rpacks/recount/data/recount_url.RData
v1.1.24 -- recount_url now includes the GTEx bigWig files
Revision: 127574
Author: z.gu
Date: 2017-03-21T16:12:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/DESCRIPTION
Modified  /trunk/madman/Rpacks/ComplexHeatmap/NAMESPACE
Modified  /trunk/madman/Rpacks/ComplexHeatmap/NEWS
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/Legend.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/annotation_fun.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/Legend.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/packLegend.rd
Merge branch 'master' into devel

* master:
  modify default gap to 4mm
  update document for packLegend()
  add packLegend()
  anno_*(): warn if input is a data frame
Revision: 127573
Author: a.chiu
Date: 2017-03-21T15:12:14+00:00
Paths:
Deleted  /trunk/madman/Rpacks/twoddpcr/tests/.DS_Store
Deleted  /trunk/madman/Rpacks/twoddpcr/tests/testthat/.DS_Store
Remove dotfiles

From: Anthony Chiu <anthony.chiu@cruk.manchester.ac.uk>
Revision: 127572
Author: t.smith
Date: 2017-03-21T15:09:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowPloidy/.Rbuildignore
Modified  /trunk/madman/Rpacks/flowPloidy/.gitignore
Modified  /trunk/madman/Rpacks/flowPloidy/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowPloidy/NAMESPACE
Modified  /trunk/madman/Rpacks/flowPloidy/R/FlowHist.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/flowAnalysis.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/flowGate.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/models.R
Added  /trunk/madman/Rpacks/flowPloidy/R/plotFlowHist.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/shiny.R
Modified  /trunk/madman/Rpacks/flowPloidy/README.md
Modified  /trunk/madman/Rpacks/flowPloidy/man/FlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/browseFlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/fhAnalyze.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/findPeaks.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/gauss.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/pickInit.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/plot.FlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/plotFH.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/setBins.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/tabulateFlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/updateFlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/viewFlowChannels.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/test-script.R
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/draw_gate.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/flowPloidy-gettingStarted.Rmd
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowPloidy-overview.Rmd
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowPloidy.bibtex
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/fpPandoc.latex
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/fw_high.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/fw_low.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gate_ui.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gated_analysis.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse1.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse11.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse11b.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse11c.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse2.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse2c.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse3.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse3b.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/gs_browse3c.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/histogram-tour.Rmd
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/nw_high.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/nw_low.png
Added  /trunk/madman/Rpacks/flowPloidy/vignettes/vac1.png
Updating to 1.1.4
Revision: 127571
Author: a.chiu
Date: 2017-03-21T15:07:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/twoddpcr/DESCRIPTION
Modified  /trunk/madman/Rpacks/twoddpcr/NAMESPACE
Modified  /trunk/madman/Rpacks/twoddpcr/R/dropletPlot.R
Modified  /trunk/madman/Rpacks/twoddpcr/R/mahRain.R
Modified  /trunk/madman/Rpacks/twoddpcr/R/relabelClasses.R
Modified  /trunk/madman/Rpacks/twoddpcr/R/shinyVisServer.R
Modified  /trunk/madman/Rpacks/twoddpcr/R/shinyVisUI.R
Modified  /trunk/madman/Rpacks/twoddpcr/README.md
Modified  /trunk/madman/Rpacks/twoddpcr/inst/NEWS
Added  /trunk/madman/Rpacks/twoddpcr/inst/rmd
Added  /trunk/madman/Rpacks/twoddpcr/inst/rmd/report-html.Rmd
Modified  /trunk/madman/Rpacks/twoddpcr/man/dropletPlot.Rd
Added  /trunk/madman/Rpacks/twoddpcr/tests/.DS_Store
Added  /trunk/madman/Rpacks/twoddpcr/tests/testthat/.DS_Store
Modified  /trunk/madman/Rpacks/twoddpcr/vignettes/twoddpcr.Rmd
Updates as suggested by anonymous reviewers.
1. Shiny app:
  * Simple dynamic HTML report generation.
  * Re-use the user-specified labels in plots and tables (where
    possible). NN, NP, PN and PP are still used internally and for file
    input/output.
  * Add captions to pages, improve the help sidebars and page.
2. Vignette:
  * Describe the KRASdata dataset.
  * Compare the classification methods with discussion.
3. Bug fixes:
  * k-means failed when only one class was present.

From: Anthony Chiu <anthony.chiu@cruk.manchester.ac.uk>

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