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Revision: 119015
Author: hpages
Date: 2016-06-29T06:20:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/src/XVectorList_class.c
Set MAX_TAG_LENGTH to 2^28 instead of 2^30, with the consequence that the mega
sequences in the "pool" slot of an XStringSet object will be <= 256 Mb, unless
the object contains elements that are longer than this limit.
Revision: 119014
Author: c.hao
Date: 2016-06-29T05:59:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/cytofkit/DESCRIPTION
Modified  /trunk/madman/Rpacks/cytofkit/NAMESPACE
Modified  /trunk/madman/Rpacks/cytofkit/R/cytof_cluster.R
Modified  /trunk/madman/Rpacks/cytofkit/R/cytof_dimensionReduction.R
Modified  /trunk/madman/Rpacks/cytofkit/R/cytof_postProcess.R
Modified  /trunk/madman/Rpacks/cytofkit/R/cytof_progression.R
Modified  /trunk/madman/Rpacks/cytofkit/R/cytofkit.R
Modified  /trunk/madman/Rpacks/cytofkit/R/cytofkit_GUI.R
Modified  /trunk/madman/Rpacks/cytofkit/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/cytofkit/inst/shiny/global.R
Modified  /trunk/madman/Rpacks/cytofkit/inst/shiny/server.R
Modified  /trunk/madman/Rpacks/cytofkit/inst/shiny/ui.R
Modified  /trunk/madman/Rpacks/cytofkit/man/cytof_clusterPlot.Rd
Added  /trunk/madman/Rpacks/cytofkit/man/cytof_clusterStat.Rd
Added  /trunk/madman/Rpacks/cytofkit/man/cytof_colorPlot.Rd
Modified  /trunk/madman/Rpacks/cytofkit/man/cytof_heatmap.Rd
Modified  /trunk/madman/Rpacks/cytofkit/man/cytof_progression.Rd
Modified  /trunk/madman/Rpacks/cytofkit/man/cytof_progressionPlot.Rd
Modified  /trunk/madman/Rpacks/cytofkit/man/cytof_writeResults.Rd
Modified  /trunk/madman/Rpacks/cytofkit/man/cytofkit.Rd
Modified  /trunk/madman/Rpacks/cytofkit/man/launchShinyAPP_GUI.Rd
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/cytofkit_GUI_mac.png
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/cytofkit_GUI_windows.png
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/cytofkit_example.Rmd
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/cytofkit_pipeline.png
Added  /trunk/madman/Rpacks/cytofkit/vignettes/cytofkit_shinyAPP.Rmd
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/cytofkit_workflow.Rmd
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/heatmap.png
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/load2shiny.png
Added  /trunk/madman/Rpacks/cytofkit/vignettes/marker_expression_profile.png
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/progressionPlot.png
Added  /trunk/madman/Rpacks/cytofkit/vignettes/run_Diffusionmap.png
Added  /trunk/madman/Rpacks/cytofkit/vignettes/run_FlowSOM.png
Modified  /trunk/madman/Rpacks/cytofkit/vignettes/scatterPlot.png
new version 1.5.5 same as release version 1.4.6
Revision: 119010
Author: x.liu
Date: 2016-06-29T02:15:53+00:00
Paths:
 /trunk/madman/Rpacks/puma/DESCRIPTION
log.message
Revision: 119009
Author: x.liu
Date: 2016-06-29T02:14:39+00:00
Paths:
 /trunk/madman/Rpacks/puma/R/igmoExon.R
log.message
Revision: 119008
Author: hpages
Date: 2016-06-28T22:32:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/R/XVectorList-class.R
Ugly workaround a serious callNextMethod inefficiency reported here:
  https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16974
Revision: 119007
Author: mtmorgan
Date: 2016-06-28T22:19:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.4.manifest
Added  /trunk/madman/Rpacks/fgsea
Added  /trunk/madman/Rpacks/fgsea/.Rbuildignore
Added  /trunk/madman/Rpacks/fgsea/.gitignore
Added  /trunk/madman/Rpacks/fgsea/.travis.yml
Added  /trunk/madman/Rpacks/fgsea/DESCRIPTION
Added  /trunk/madman/Rpacks/fgsea/LICENCE
Added  /trunk/madman/Rpacks/fgsea/NAMESPACE
Added  /trunk/madman/Rpacks/fgsea/R
Added  /trunk/madman/Rpacks/fgsea/R/RcppExports.R
Added  /trunk/madman/Rpacks/fgsea/R/fgsea-package.R
Added  /trunk/madman/Rpacks/fgsea/R/fgsea.R
Added  /trunk/madman/Rpacks/fgsea/R/pathways.R
Added  /trunk/madman/Rpacks/fgsea/R/plot.R
Added  /trunk/madman/Rpacks/fgsea/README.md
Added  /trunk/madman/Rpacks/fgsea/data
Added  /trunk/madman/Rpacks/fgsea/data/examplePathways.rda
Added  /trunk/madman/Rpacks/fgsea/data/exampleRanks.rda
Added  /trunk/madman/Rpacks/fgsea/data-raw
Added  /trunk/madman/Rpacks/fgsea/data-raw/examplePathways.R
Added  /trunk/madman/Rpacks/fgsea/data-raw/exampleRanks.R
Added  /trunk/madman/Rpacks/fgsea/fgsea.Rproj
Added  /trunk/madman/Rpacks/fgsea/inst
Added  /trunk/madman/Rpacks/fgsea/inst/extdata
Added  /trunk/madman/Rpacks/fgsea/inst/extdata/fgsea_res.tsv
Added  /trunk/madman/Rpacks/fgsea/inst/extdata/mouse.reactome.gmt
Added  /trunk/madman/Rpacks/fgsea/inst/extdata/naive.vs.th1.rnk
Added  /trunk/madman/Rpacks/fgsea/inst/gen_gene_ranks.R
Added  /trunk/madman/Rpacks/fgsea/inst/gene_reactome_pathways.R
Added  /trunk/madman/Rpacks/fgsea/inst/th1_gsea.R
Added  /trunk/madman/Rpacks/fgsea/man
Added  /trunk/madman/Rpacks/fgsea/man/calcGseaStat.Rd
Added  /trunk/madman/Rpacks/fgsea/man/calcGseaStatCumulative.Rd
Added  /trunk/madman/Rpacks/fgsea/man/examplePathways.Rd
Added  /trunk/madman/Rpacks/fgsea/man/exampleRanks.Rd
Added  /trunk/madman/Rpacks/fgsea/man/fgsea.Rd
Added  /trunk/madman/Rpacks/fgsea/man/gmtPathways.Rd
Added  /trunk/madman/Rpacks/fgsea/man/plotEnrichment.Rd
Added  /trunk/madman/Rpacks/fgsea/man/plotGseaTable.Rd
Added  /trunk/madman/Rpacks/fgsea/man/reactomePathways.Rd
Added  /trunk/madman/Rpacks/fgsea/src
Added  /trunk/madman/Rpacks/fgsea/src/RcppExports.cpp
Added  /trunk/madman/Rpacks/fgsea/src/fastGSEA.cpp
Added  /trunk/madman/Rpacks/fgsea/src/fastGSEA.h
Added  /trunk/madman/Rpacks/fgsea/src/fgsea_init.c
Added  /trunk/madman/Rpacks/fgsea/test.R
Added  /trunk/madman/Rpacks/fgsea/tests
Added  /trunk/madman/Rpacks/fgsea/tests/testthat
Added  /trunk/madman/Rpacks/fgsea/tests/testthat/test_gsea_analysis.R
Added  /trunk/madman/Rpacks/fgsea/tests/testthat/test_gsea_stat.R
Added  /trunk/madman/Rpacks/fgsea/tests/testthat/test_pathways.R
Added  /trunk/madman/Rpacks/fgsea/tests/testthat/test_plot.R
Added  /trunk/madman/Rpacks/fgsea/tests/testthat.R
Added  /trunk/madman/Rpacks/fgsea/vignettes
Added  /trunk/madman/Rpacks/fgsea/vignettes/fgsea-tutorial.Rmd
Adding fgsea
Revision: 119006
Author: m.lawrence
Date: 2016-06-28T22:07:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
version bump
Revision: 119005
Author: mtmorgan
Date: 2016-06-28T21:55:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.4.manifest
Added  /trunk/madman/Rpacks/ccmap
Added  /trunk/madman/Rpacks/ccmap/DESCRIPTION
Added  /trunk/madman/Rpacks/ccmap/LICENSE
Added  /trunk/madman/Rpacks/ccmap/NAMESPACE
Added  /trunk/madman/Rpacks/ccmap/R
Added  /trunk/madman/Rpacks/ccmap/R/predict_combos.R
Added  /trunk/madman/Rpacks/ccmap/R/query_drugs.R
Added  /trunk/madman/Rpacks/ccmap/R/query_utils.R
Added  /trunk/madman/Rpacks/ccmap/README.md
Added  /trunk/madman/Rpacks/ccmap/inst
Added  /trunk/madman/Rpacks/ccmap/man
Added  /trunk/madman/Rpacks/ccmap/man/get_dprimes.Rd
Added  /trunk/madman/Rpacks/ccmap/man/predict_combos.Rd
Added  /trunk/madman/Rpacks/ccmap/man/query_drugs.Rd
Added  /trunk/madman/Rpacks/ccmap/man/sum_rowcolCumsum.Rd
Added  /trunk/madman/Rpacks/ccmap/tests
Added  /trunk/madman/Rpacks/ccmap/tests/testthat
Added  /trunk/madman/Rpacks/ccmap/tests/testthat/test-all.R
Added  /trunk/madman/Rpacks/ccmap/tests/testthat.R
Added  /trunk/madman/Rpacks/ccmap/vignettes
Added  /trunk/madman/Rpacks/ccmap/vignettes/accuracy.png
Added  /trunk/madman/Rpacks/ccmap/vignettes/ccmap-vignette.Rmd
Added  /trunk/madman/Rpacks/ccmap/vignettes/meta-vs-cons.png
Added  /trunk/madman/Rpacks/qsea
Added  /trunk/madman/Rpacks/qsea/DESCRIPTION
Added  /trunk/madman/Rpacks/qsea/NAMESPACE
Added  /trunk/madman/Rpacks/qsea/NEWS
Added  /trunk/madman/Rpacks/qsea/R
Added  /trunk/madman/Rpacks/qsea/R/qsea-classes.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.addCNV.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.createSet.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.example.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.genomeWindows.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.getCoverage.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.glm.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.makeTable.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.normalize.R
Added  /trunk/madman/Rpacks/qsea/R/qsea.plots.R
Added  /trunk/madman/Rpacks/qsea/R/sysdata.rda
Added  /trunk/madman/Rpacks/qsea/inst
Added  /trunk/madman/Rpacks/qsea/man
Added  /trunk/madman/Rpacks/qsea/man/addCNV.Rd
Added  /trunk/madman/Rpacks/qsea/man/addContrast.Rd
Added  /trunk/madman/Rpacks/qsea/man/addCoverage.Rd
Added  /trunk/madman/Rpacks/qsea/man/addEnrichmentParameters.Rd
Added  /trunk/madman/Rpacks/qsea/man/addLibraryFactors.Rd
Added  /trunk/madman/Rpacks/qsea/man/addOffset.Rd
Added  /trunk/madman/Rpacks/qsea/man/addPatternDensity.Rd
Added  /trunk/madman/Rpacks/qsea/man/addSeqPref.Rd
Added  /trunk/madman/Rpacks/qsea/man/createQseaSet.Rd
Added  /trunk/madman/Rpacks/qsea/man/example.Rd
Added  /trunk/madman/Rpacks/qsea/man/fitNBglm.Rd
Added  /trunk/madman/Rpacks/qsea/man/getPCA.Rd
Added  /trunk/madman/Rpacks/qsea/man/isSignificant.Rd
Added  /trunk/madman/Rpacks/qsea/man/makeTable.Rd
Added  /trunk/madman/Rpacks/qsea/man/normMethod.Rd
Added  /trunk/madman/Rpacks/qsea/man/plotCNV.Rd
Added  /trunk/madman/Rpacks/qsea/man/plotCoverage.Rd
Added  /trunk/madman/Rpacks/qsea/man/plotEnrichmentProfile.Rd
Added  /trunk/madman/Rpacks/qsea/man/plotPCA.Rd
Added  /trunk/madman/Rpacks/qsea/man/qsea-package.Rd
Added  /trunk/madman/Rpacks/qsea/man/qseaGLM-class.Rd
Added  /trunk/madman/Rpacks/qsea/man/qseaPCA-class.Rd
Added  /trunk/madman/Rpacks/qsea/man/qseaSet-class.Rd
Added  /trunk/madman/Rpacks/qsea/man/regionStats.Rd
Added  /trunk/madman/Rpacks/qsea/src
Added  /trunk/madman/Rpacks/qsea/src/lm.c
Added  /trunk/madman/Rpacks/qsea/tests
Added  /trunk/madman/Rpacks/qsea/tests/testthat
Added  /trunk/madman/Rpacks/qsea/tests/testthat/test_example.R
Added  /trunk/madman/Rpacks/qsea/tests/testthat/test_glm.R
Added  /trunk/madman/Rpacks/qsea/tests/testthat.R
Added  /trunk/madman/Rpacks/qsea/vignettes
Added  /trunk/madman/Rpacks/qsea/vignettes/qseaTutorial.bib
Added  /trunk/madman/Rpacks/qsea/vignettes/qsea_tutorial.Rmd
Adding ccmap, qsea
Revision: 119004
Author: mtmorgan
Date: 2016-06-28T21:42:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.4.manifest
Added  /trunk/madman/Rpacks/normr
Added  /trunk/madman/Rpacks/normr/DESCRIPTION
Added  /trunk/madman/Rpacks/normr/NAMESPACE
Added  /trunk/madman/Rpacks/normr/NEWS
Added  /trunk/madman/Rpacks/normr/R
Added  /trunk/madman/Rpacks/normr/R/NormRCountConfig.R
Added  /trunk/madman/Rpacks/normr/R/NormRFit.R
Added  /trunk/madman/Rpacks/normr/R/RcppExports.R
Added  /trunk/madman/Rpacks/normr/R/methods.R
Added  /trunk/madman/Rpacks/normr/README.md
Added  /trunk/madman/Rpacks/normr/inst
Added  /trunk/madman/Rpacks/normr/inst/examples
Added  /trunk/madman/Rpacks/normr/inst/examples/NormRCountConfig_example.R
Added  /trunk/madman/Rpacks/normr/inst/examples/NormRFit_example.R
Added  /trunk/madman/Rpacks/normr/inst/examples/methods_example.R
Added  /trunk/madman/Rpacks/normr/inst/extdata
Added  /trunk/madman/Rpacks/normr/inst/extdata/1a.png
Added  /trunk/madman/Rpacks/normr/inst/extdata/1b.png
Added  /trunk/madman/Rpacks/normr/inst/extdata/2.png
Added  /trunk/madman/Rpacks/normr/inst/extdata/3.png
Added  /trunk/madman/Rpacks/normr/inst/extdata/K562_H3K36me3.bam
Added  /trunk/madman/Rpacks/normr/inst/extdata/K562_H3K36me3.bam.bai
Added  /trunk/madman/Rpacks/normr/inst/extdata/K562_H3K4me3.bam
Added  /trunk/madman/Rpacks/normr/inst/extdata/K562_H3K4me3.bam.bai
Added  /trunk/madman/Rpacks/normr/inst/extdata/K562_Input.bam
Added  /trunk/madman/Rpacks/normr/inst/extdata/K562_Input.bam.bai
Added  /trunk/madman/Rpacks/normr/inst/extdata/bamgeneration
Added  /trunk/madman/Rpacks/normr/inst/extdata/genes.bed
Added  /trunk/madman/Rpacks/normr/inst/extdata/header.sam
Added  /trunk/madman/Rpacks/normr/man
Added  /trunk/madman/Rpacks/normr/man/NormRCountConfig-class.Rd
Added  /trunk/madman/Rpacks/normr/man/NormRFit-class.Rd
Added  /trunk/madman/Rpacks/normr/man/normR-diffR.Rd
Added  /trunk/madman/Rpacks/normr/man/normR-enrichR.Rd
Added  /trunk/madman/Rpacks/normr/man/normR-regimeR.Rd
Added  /trunk/madman/Rpacks/normr/man/normR.Rd
Added  /trunk/madman/Rpacks/normr/src
Added  /trunk/madman/Rpacks/normr/src/Makevars
Added  /trunk/madman/Rpacks/normr/src/RcppExports.cpp
Added  /trunk/madman/Rpacks/normr/src/em.cpp
Added  /trunk/madman/Rpacks/normr/src/normr_init.c
Added  /trunk/madman/Rpacks/normr/tests
Added  /trunk/madman/Rpacks/normr/tests/testthat
Added  /trunk/madman/Rpacks/normr/tests/testthat/test-CLI.R
Added  /trunk/madman/Rpacks/normr/tests/testthat/test-NormRFit.R
Added  /trunk/madman/Rpacks/normr/tests/testthat/test-methods.R
Added  /trunk/madman/Rpacks/normr/tests/testthat/utils.R
Added  /trunk/madman/Rpacks/normr/tests/testthat.R
Added  /trunk/madman/Rpacks/normr/vignettes
Added  /trunk/madman/Rpacks/normr/vignettes/normr.Rmd
Adding normr
Revision: 119002
Author: mtmorgan
Date: 2016-06-28T18:37:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
import methods

- "new" used extensively
Revision: 119001
Author: a.oles
Date: 2016-06-28T16:37:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/inst/resources/tex/Bioconductor2.sty
version 2.1.14
- be more explicit about color specification in section titles to address the issue with color spilling out on margin notes

From: aoles <andrzej.oles@gmail.com>
Revision: 119000
Author: b.mifsud
Date: 2016-06-28T16:09:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOTHiC/R/GOTHiC.R
fix naming of quality plot
Revision: 118998
Author: m.lawrence
Date: 2016-06-28T14:49:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
move knitr and devtools to suggests
Revision: 118997
Author: m.lawrence
Date: 2016-06-28T14:46:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/NAMESPACE
Modified  /trunk/madman/Rpacks/biocViews/R/getPackNames.R
Modified  /trunk/madman/Rpacks/biocViews/R/repository.R
make knitr dependency optional
Revision: 118996
Author: t.hardcastle
Date: 2016-06-28T12:37:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/baySeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/baySeq/R/bimodalSeparator.R
Modified  /trunk/madman/Rpacks/baySeq/R/countData-accessors.R
Modified  /trunk/madman/Rpacks/baySeq/R/topCounts.R
Modified  /trunk/madman/Rpacks/baySeq/man/topCounts.Rd
1.7.1 optimised bimodal separator, change to topCounts so that selection by likelihood, FDR and FWER are ANDed rather than exclusive.
Revision: 118995
Author: t.hardcastle
Date: 2016-06-28T12:25:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/riboSeqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/riboSeqR/R/plotTranscript.R
Modified  /trunk/madman/Rpacks/riboSeqR/vignettes/riboSeqR.tex
1.7.1 plotTranscripts was using a different y-axis for first plot. This was weird.
Revision: 118994
Author: a.oles
Date: 2016-06-28T11:55:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/inst/resources/tex/Bioconductor2.sty
version 2.1.13
- load 'marginfix' LaTeX package to prevent margin notes from overflowing the bottom margin
- pass option `multiple` to 'footmisc' for better handling of consecutive footnotes

From: aoles <andrzej.oles@gmail.com>
Revision: 118993
Author: a.conesa
Date: 2016-06-28T11:40:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/maSigPro/DESCRIPTION
mclust in description 
Revision: 118992
Author: r.castelo
Date: 2016-06-28T09:56:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/annotationEngine.R
Bugfix to avoid trying to score splice sites overlapping non-SNVs.

From: [rcastelo] <[robert.castelo@upf.edu]>
Revision: 118990
Author: smyth
Date: 2016-06-28T08:32:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/R/combine.R
Modified  /trunk/madman/Rpacks/limma/R/geneset-camera.R
Modified  /trunk/madman/Rpacks/limma/R/geneset-fry.R
Modified  /trunk/madman/Rpacks/limma/R/geneset-roast.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
28 Jun 2016: limma 3.29.14

- Bug fix for fry() when 'index' has NULL names.
Revision: 118985
Author: g.yu
Date: 2016-06-28T06:26:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/NAMESPACE
Modified  /trunk/madman/Rpacks/ggtree/R/experimental_function.R
Modified  /trunk/madman/Rpacks/ggtree/R/ggtree.R
Added  /trunk/madman/Rpacks/ggtree/R/method-identify.R
Added  /trunk/madman/Rpacks/ggtree/man/identify.Rd
identify method for ggtree
Revision: 118983
Author: s.han2
Date: 2016-06-28T05:22:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/IVAS/DESCRIPTION
Modified  /trunk/madman/Rpacks/IVAS/NAMESPACE
Modified  /trunk/madman/Rpacks/IVAS/NEWS
Modified  /trunk/madman/Rpacks/IVAS/R/MsqtlFinder.R
Modified  /trunk/madman/Rpacks/IVAS/R/calSignificant.R
Modified  /trunk/madman/Rpacks/IVAS/R/findAlternative.R
Modified  /trunk/madman/Rpacks/IVAS/R/saveBplot.R
Modified  /trunk/madman/Rpacks/IVAS/R/sqtlfinder.R
- Debug error when result is NULL in the MsqtlFinder.
- Adjust Chr names between GTF and SNP locus data.
- Change test of UTR region.
- Debug error in Boxplot, calSignificant and sqtlfinder.
Revision: 118981
Author: g.yu
Date: 2016-06-28T04:50:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/enrichKEGG.R
Modified  /trunk/madman/Rpacks/clusterProfiler/README.md
fixed duplicated path for ko
Revision: 118977
Author: hpages
Date: 2016-06-28T01:01:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/R/XVector-class.R
Modified  /trunk/madman/Rpacks/XVector/R/XVectorList-class.R
Reduce by half fixed overhead of "extractROWS" method for XVectorList (called
internally when subsetting an XStringSet object).
Revision: 118973
Author: m.lawrence
Date: 2016-06-27T20:05:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VRanges-class.R
fix check for FILT == "PASS"
Revision: 118972
Author: h.zare
Date: 2016-06-27T19:06:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/Pigengene/DESCRIPTION
Modified  /trunk/madman/Rpacks/Pigengene/R/compute.pigengene.R
browser removed
Revision: 118966
Author: a.conesa
Date: 2016-06-27T07:36:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/maSigPro/DESCRIPTION
mclust in description 
Revision: 118962
Author: l.gatto
Date: 2016-06-26T12:08:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/ProteomicsAnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/ProteomicsAnnotationHubData/NEWS
Modified  /trunk/madman/Rpacks/ProteomicsAnnotationHubData/vignettes/ProteomicsAnnotationHubData.Rmd
fix conflicts

From: Laurent <lg390@cam.ac.uk>
Revision: 118959
Author: smyth
Date: 2016-06-26T06:14:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/R/plots-fit.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
26 Jun 2016: limma 3.29.13

- The lowess line drawn by plotSA() is now more robust with respect
  to NA variances.
Revision: 118958
Author: s.bagaria
Date: 2016-06-26T03:07:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/GoogleGenomics/.travis.yml
Modified  /trunk/madman/Rpacks/GoogleGenomics/NAMESPACE
Switch to native Travis (container-based) support for R.

From: Siddhartha Bagaria <sidb@google.com>
Revision: 118957
Author: m.riester
Date: 2016-06-26T02:36:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Another version bump to 1.1.28.
Revision: 118956
Author: m.riester
Date: 2016-06-26T02:35:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Added code to vignette to download repeat regions from UCSC.
Revision: 118954
Author: mtmorgan
Date: 2016-06-25T23:37:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/R/zzz.R
Modified  /trunk/madman/Rpacks/BiocInstaller/inst/scripts/BiocInstaller.dcf
bugfix: Bioc 3.3 support for R-3.3.1
Revision: 118953
Author: m.riester
Date: 2016-06-25T22:31:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Updated vignette with new BED file variant filtering.
Revision: 118951
Author: m.riester
Date: 2016-06-25T21:51:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/filterVcf.R
Added  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_filterVcf.R
Allow filtering of SNPs by BED files via snp.blacklist.
Revision: 118950
Author: m.love
Date: 2016-06-25T16:51:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
add coord_fixed() to vignette (already in plotpca)
Revision: 118949
Author: h.fang
Date: 2016-06-25T16:51:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/INSTALLATIONs.md
Bump to the version 1.11.1
Revision: 118944
Author: hpages
Date: 2016-06-25T04:38:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
add hgu95av2probe to Suggests (used in new "10 Things You Didn't Know" slides)
Revision: 118943
Author: hpages
Date: 2016-06-25T03:42:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/absoluteRanges.Rd
Added  /trunk/madman/Rpacks/GenomicRanges/vignettes/10_things_you_didnt_know.Rnw
add "10 Things You Didn't Know" slides (from BioC 2016 conf)
Revision: 118941
Author: l.zhu
Date: 2016-06-24T21:38:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/GUIDEseq/NAMESPACE
Modified  /trunk/madman/Rpacks/GUIDEseq/R/combineOfftargets.R
Modified  /trunk/madman/Rpacks/GUIDEseq/man/combineOfftargets.Rd
added venn diagram and test data for combineOfftargets.R
Revision: 118940
Author: m.riester
Date: 2016-06-24T20:52:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Updated vignette.
Revision: 118939
Author: m.riester
Date: 2016-06-24T19:57:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Added expected b-allele frequencies to plotAbs, type=BAF.
Revision: 118937
Author: a.oles
Date: 2016-06-24T12:59:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Version bump to trigger vignette rebuild after updates to BiocStyle
Revision: 118936
Author: a.oles
Date: 2016-06-24T12:06:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/pdf_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/utils.R
version 2.1.12
- remove unintended dependency on 'knitr' (https://github.com/Bioconductor/BiocStyle/issues/2)

From: aoles <andrzej.oles@gmail.com>
Revision: 118933
Author: h.fang
Date: 2016-06-24T11:04:17+00:00
Paths:
Added  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Bump to the version 1.10.1
Revision: 118932
Author: h.fang
Date: 2016-06-24T11:03:50+00:00
Paths:
Deleted  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Bump to the version 1.10.1
Revision: 118930
Author: h.fang
Date: 2016-06-24T11:00:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Bump to the version 1.10.1
Revision: 118929
Author: h.fang
Date: 2016-06-24T10:59:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Bump to the version 1.10.1
Revision: 118928
Author: a.lun
Date: 2016-06-24T08:06:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/InteractionSet/DESCRIPTION
Modified  /trunk/madman/Rpacks/InteractionSet/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/InteractionSet/tests/testthat/test-link.R
Forced test-link.R to use base::merge.
Revision: 118924
Author: g.yu
Date: 2016-06-24T01:50:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterProfiler/README.md
typo
Revision: 118922
Author: h.zare
Date: 2016-06-24T00:58:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/Pigengene/DESCRIPTION
Modified  /trunk/madman/Rpacks/Pigengene/R/compute.pigengene.R
Modified  /trunk/madman/Rpacks/Pigengene/R/project.eigen.R
minor edits in project.eigen messages
Revision: 118921
Author: r.uriarte
Date: 2016-06-23T23:30:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/OncoSimulR/DESCRIPTION
Modified  /trunk/madman/Rpacks/OncoSimulR/inst/NEWS
Modified  /trunk/madman/Rpacks/OncoSimulR/tests/testthat/test.mutator.R
Modified  /trunk/madman/Rpacks/OncoSimulR/vignettes/gitHeadInfo.gin
v. 2.3.4: fixed tests failing on Win 32-bit
Revision: 118918
Author: m.jiang
Date: 2016-06-23T23:23:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClust/DESCRIPTION
bump
Revision: 118917
Author: m.jiang
Date: 2016-06-23T23:23:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClust/man/flowClust.Rd
Modified  /trunk/madman/Rpacks/flowClust/man/tmixFilter.Rd
update Rd files to fix bioc warnings
Revision: 118916
Author: m.jiang
Date: 2016-06-23T22:59:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/DESCRIPTION
Modified  /trunk/madman/Rpacks/openCyto/man/quadGate.tmix.Rd
update doc to fix bioc warning
Revision: 118915
Author: m.riester
Date: 2016-06-23T19:50:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_autoCurateResults.R
Added test for getDiploid crash.

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