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Revision: 105874
Author: g.yu
Date: 2015-07-07T09:27:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/R/readPeakFile.R
fixed chromEnd
Revision: 105866
Author: x.zheng
Date: 2015-07-07T07:40:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/README.md
Added  /trunk/madman/Rpacks/SeqArray/inst/unitTests/test_examples.R
Modified  /trunk/madman/Rpacks/SeqArray/man/seqParallel.Rd
Modified  /trunk/madman/Rpacks/SeqArray/src/ConvVCF2GDS.cpp
Modified  /trunk/madman/Rpacks/SeqArray/tests/test.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0097287ced79730c505712720c874cc37fd4ea7b

    increase test coverage

Revision: 105864
Author: n.aghaeepour
Date: 2015-07-07T02:50:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowMeans/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowMeans/R/flowMeans.R
bumping version number
Revision: 105863
Author: n.aghaeepour
Date: 2015-07-07T02:41:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowMeans/R/flowMeans.R
Fixed another small NumC related bug.
Revision: 105862
Author: n.aghaeepour
Date: 2015-07-07T02:30:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowMeans/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowMeans/R/flowMeans.R
Fixing NumC bug that was removed during the BioC/runtime issue.
Revision: 105861
Author: l.zhu
Date: 2015-07-07T02:24:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/R/findgRNAs.R
fixed a typo
Revision: 105859
Author: x.zheng
Date: 2015-07-06T23:46:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/HIBAG/.travis.yml
Modified  /trunk/madman/Rpacks/HIBAG/README.md
Modified  /trunk/madman/Rpacks/HIBAG/tests/runTests.R
Modified  /trunk/madman/Rpacks/HIBAG/vignettes/HIBAG_Tutorial_html.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 049f4535793aafc58e301fe400950ac3d26aa90e

    increase test coverage

Revision: 105857
Author: x.zheng
Date: 2015-07-06T22:43:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/.travis.yml
Modified  /trunk/madman/Rpacks/gdsfmt/man/showfile.gds.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: d127b09515cf8c0fee00196e8fef7601c6bf38ea

    not able to run codecov on Travis (coverage will be uploaded from local machine)

Revision: 105856
Author: c.wu
Date: 2015-07-06T22:31:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/mygene/DESCRIPTION
bumped version
Revision: 105855
Author: z.gu
Date: 2015-07-06T22:31:20+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/Heatmap-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/utils.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/AdditiveUnit-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/AdditiveUnit.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/ColorMapping-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/ColorMapping.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/Heatmap-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/Heatmap.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/HeatmapAnnotation-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/HeatmapAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/HeatmapList-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/HeatmapList.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/SingleAnnotation-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/SingleAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/add.AdditiveUnit.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/add_heatmap-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/add_heatmap-HeatmapAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/add_heatmap-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/anno_barplot.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/anno_boxplot.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/anno_density.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/anno_histogram.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/anno_points.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/anno_text.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/annotation_legend_size-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/color_mapping_legend-ColorMapping-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/columnAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/component_height-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/component_height-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/component_width-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/component_width-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/dist2.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-HeatmapAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-SingleAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_annotation-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_annotation_legend-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_dimnames-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_hclust-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_heatmap_body-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_heatmap_legend-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_heatmap_list-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_title-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_title-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/get_color_mapping_list-HeatmapAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/grid.dendrogram.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/heatmap_legend_size-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_column_cluster-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_layout-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_layout-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_row_cluster-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/map_to_colors-ColorMapping-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/plot.HeatmapList.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/plotDataFrame.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/prepare-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/print.HeatmapList.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/rowAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/set_component_height-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/show-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/show-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/ComplexHeatmap.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2786dac4ddaa97c69cc24e29e121ed1a1624cdf4

    Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: a61c101325601aa0d4d3ba81e10c33d4a8b34c63

    rows can be split if providing a clustering object

Revision: 105854
Author: s.arora
Date: 2015-07-06T22:17:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
code update

- readyToAdd() now returns package names based on  'pre-accepted'
- creditowrthy() prints outs to the template which is t be included in
  weekly report.
Revision: 105853
Author: c.wu
Date: 2015-07-06T21:38:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/mygene/R/mygene.R
fixed httr update compatibility
Revision: 105852
Author: x.zheng
Date: 2015-07-06T21:36:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: cee4088cf1ee6285682ab90c59d8d3f93be05936

    update .travis.yml to create test coverage information

Revision: 105848
Author: khansen
Date: 2015-07-06T21:02:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/R/preprocessFunnorm.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 431aed92694e93cd387ddc8ea0ec583797bc266a

    Merge pull request #27 from Jfortin1/patch-2

    Added the condition nPCs > 0

Commit id: 71ea076d12c34172bd4a6ee4fbdb97f8d676bcd0

    Added the condition nPCs > 0

Revision: 105846
Author: khansen
Date: 2015-07-06T21:00:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1fec54ca6135357a2399473f5caffa57cbd16313

    Merge pull request #28 from Jfortin1/patch-3

    Added A/B compartments citation

Commit id: 18b2b39fd97edd5f5f9a07cb374a1e8c4332547e

    Added A/B compartments citation

Revision: 105845
Author: s.gogarten
Date: 2015-07-06T20:47:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GWASTools/R/createDataFile.R
Modified  /trunk/madman/Rpacks/GWASTools/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/GWASTools/inst/unitTests/createDataFile_test.R
Modified  /trunk/madman/Rpacks/GWASTools/man/createDataFile.Rd
allow character scanID in createDataFile
Revision: 105844
Author: x.zheng
Date: 2015-07-06T20:35:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f772da2e8d32d4dde12f1e91230efe514685ad30

    Update .travis.yml

Revision: 105843
Author: s.munro
Date: 2015-07-06T18:58:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/erccdashboard/DESCRIPTION
Modified  /trunk/madman/Rpacks/erccdashboard/NEWS
test commit take 2

From: munrosa <sarah.munro@nist.gov>
Revision: 105842
Author: m.jiang
Date: 2015-07-06T18:03:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/DESCRIPTION
Modified  /trunk/madman/Rpacks/openCyto/R/AllClasses.R
Modified  /trunk/madman/Rpacks/openCyto/R/add_pop.R
Modified  /trunk/madman/Rpacks/openCyto/R/csvTemplate-parser.R
Modified  /trunk/madman/Rpacks/openCyto/inst/tests/gating-testSuite.R
Modified  /trunk/madman/Rpacks/openCyto/man/add_pop.Rd
Modified  /trunk/madman/Rpacks/openCyto/man/gatingTemplate-class.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9699aec060c561c52458381a36e034ca30d665d1

    skip validity check(special characters) on the alias column of the existing nodes in add_pop

Revision: 105841
Author: m.smith
Date: 2015-07-06T17:35:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/IONiseR
Modified  /trunk/madman/Rpacks/IONiseR/DESCRIPTION
Modified  /trunk/madman/Rpacks/IONiseR/R/fast5Readers.R
Modified  /trunk/madman/Rpacks/IONiseR/R/readSummary.R
Improved error handling when fast5 files are invalid.
Revision: 105840
Author: n.hayden
Date: 2015-07-06T16:49:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/NEWS
mention pileup changes in NEWS
Revision: 105832
Author: n.delhomme
Date: 2015-07-06T14:00:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/man/easyRNASeq-package.Rd
Fixed a GRanges API change identified and fixed by Michael Dondrup. Thanks
Revision: 105831
Author: n.delhomme
Date: 2015-07-06T14:00:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/NEWS
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-annotation.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-internal-methods.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-package.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-simpleRNASeq.R
Fixed a GRanges API change identified and fixed by Michael Dondrup. Thanks
Revision: 105828
Author: a.lun
Date: 2015-07-06T08:27:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/R/basefun.R
Modified  /trunk/madman/Rpacks/csaw/R/getPESizes.R
Modified  /trunk/madman/Rpacks/csaw/inst/NEWS.Rd
Switched to mapqFilter in scanBam.
Revision: 105827
Author: t.peters
Date: 2015-07-06T01:46:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/DMRcate/DESCRIPTION
Modified  /trunk/madman/Rpacks/DMRcate/NAMESPACE
Added  /trunk/madman/Rpacks/DMRcate/R/asyApply.R
Added  /trunk/madman/Rpacks/DMRcate/R/callDMRs.R
Added  /trunk/madman/Rpacks/DMRcate/R/coercions.R
Added  /trunk/madman/Rpacks/DMRcate/R/collapseAtDMRs.R
Added  /trunk/madman/Rpacks/DMRcate/R/collapseMatrix.R
Added  /trunk/madman/Rpacks/DMRcate/R/collapseNames.R
Added  /trunk/madman/Rpacks/DMRcate/R/cox.annotate.R
Modified  /trunk/madman/Rpacks/DMRcate/R/dmrcate.R
Added  /trunk/madman/Rpacks/DMRcate/R/dmrcateByChr.R
Added  /trunk/madman/Rpacks/DMRcate/R/dmrcateChr.R
Modified  /trunk/madman/Rpacks/DMRcate/R/extractCoords.R
Modified  /trunk/madman/Rpacks/DMRcate/R/extractRanges.R
Added  /trunk/madman/Rpacks/DMRcate/R/fitByChrom.R
Added  /trunk/madman/Rpacks/DMRcate/R/fitByCpG.R
Added  /trunk/madman/Rpacks/DMRcate/R/fitChrom.R
Added  /trunk/madman/Rpacks/DMRcate/R/generics.R
Added  /trunk/madman/Rpacks/DMRcate/R/getDMRdepth.R
Added  /trunk/madman/Rpacks/DMRcate/R/getDMRsAndVMRs.R
Added  /trunk/madman/Rpacks/DMRcate/R/getSharedSegments.R
Added  /trunk/madman/Rpacks/DMRcate/R/getSimpleMethHeatMap.R
Added  /trunk/madman/Rpacks/DMRcate/R/prepM.R
Added  /trunk/madman/Rpacks/DMRcate/R/prepMvals.R
Added  /trunk/madman/Rpacks/DMRcate/R/print.dmrcate.output.R
Added  /trunk/madman/Rpacks/DMRcate/README.md
Added  /trunk/madman/Rpacks/DMRcate/data
Added  /trunk/madman/Rpacks/DMRcate/data/seqinfo.hg19.rda
Commit made by the Bioconductor Git-SVN bridge.

Commit id: ebfead988c0e9cb0a4be71cd37ce273fc311fabf

    Merge pull request #1 from ttriche/master

    A few patches

Commit id: c6e51f2ba5db44a0f28e455f1dc671cc190a0ee5

    add devtools, git2r to install directions


Commit id: ba9e160fdc392c38151d892276d6ff9c74d39783

    add devtools


Commit id: 65da44588db6674a8508ea2322f0319c3ad04101

    Add explicit installation directions


Commit id: 4d4013ef941e2ec796836ef4b437c41c04a7004a

    Create README.md


Commit id: 984ea2072c68f3726491052d1bc4af128fb1063f

    initial checkin of patches to mainstream DMRcate

Revision: 105825
Author: t.girke
Date: 2015-07-06T00:58:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/Makefile
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f816aa1c7a8585e0c58c28de6369b790ad892f98

    VAR-seq updates

Revision: 105822
Author: t.girke
Date: 2015-07-06T00:26:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/README
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 83471e36993b729b128a0d1168a0499ad4b39326

    VAR-seq updates

Revision: 105821
Author: t.girke
Date: 2015-07-06T00:25:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/R/varseq.R
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/sambcf_run.sh
Modified  /trunk/madman/Rpacks/systemPipeR/man/filterVars.Rd
Modified  /trunk/madman/Rpacks/systemPipeR/man/variantReport.Rd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeVARseq.Rnw
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f26fc793e7448f6726ec3d36c7cf61209a952af6

    VAR-seq updates

Revision: 105818
Author: t.girke
Date: 2015-07-04T23:54:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/sambcf_run.sh
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f2c73e22ca9fe86405ebc78a3aa41302e874ffe0

    sam para file update

Revision: 105816
Author: t.girke
Date: 2015-07-04T22:09:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/R/developerFct.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 51efad6eaa9020c851e02158143fedb91bc0ce2b

    update of non-user functions

Revision: 105815
Author: m.love
Date: 2015-07-04T16:28:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_factors.R
fixing the factor test
Revision: 105813
Author: v.obenchain
Date: 2015-07-04T15:31:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
version bump
Revision: 105812
Author: v.obenchain
Date: 2015-07-04T15:31:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_predictCoding-methods.R
update unit tests with new VARCODON behavior
Revision: 105809
Author: v.obenchain
Date: 2015-07-04T15:16:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/predictCoding-methods.Rd
change man page wording
Revision: 105808
Author: v.obenchain
Date: 2015-07-04T15:11:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/predictCoding-methods.Rd
update man page description of VARCODON; substitution is shown even if not
translated
Revision: 105805
Author: v.obenchain
Date: 2015-07-04T14:37:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-predictCoding.R
return non-translated characters in VARCODON predictCoding() output
Revision: 105803
Author: v.obenchain
Date: 2015-07-04T14:07:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-predictCoding.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/predictCoding-methods.Rd
add ".", "+", and "-" to allowed but not translated group for predictCoding()
Revision: 105801
Author: n.delhomme
Date: 2015-07-04T10:02:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/NAMESPACE
Modified  /trunk/madman/Rpacks/easyRNASeq/NEWS
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-counts.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-internal-counts.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-normalize.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-package.R
Modified  /trunk/madman/Rpacks/easyRNASeq/man/easyRNASeq-package.Rd
Ported the version 2.4.3 changes to the development version - merge of the aggregate generics into that of the stats package
Revision: 105800
Author: n.delhomme
Date: 2015-07-04T10:02:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/NAMESPACE
Roxygen updated NAMESPACE
Revision: 105799
Author: b.knapp
Date: 2015-07-04T09:17:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/DESCRIPTION
update maintainer
Revision: 105798
Author: b.knapp
Date: 2015-07-04T09:12:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/lpNet/inst/NEWS
update maintainer
Revision: 105796
Author: dupan
Date: 2015-07-04T03:46:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/lumi/DESCRIPTION
Modified  /trunk/madman/Rpacks/lumi/R/methylation_preprocessing.R
Modified  /trunk/madman/Rpacks/lumi/man/lumiMethyR.Rd
minor update of lumiMethyR function (including all parameters of methylumiR as the parameter of lumiMethyR)
Revision: 105794
Author: t.girke
Date: 2015-07-04T01:15:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/README
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rnw
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.pdf
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 5ccc9e79dc7c7f0953a833fd3a62c371084a0b0c

    vignette updates

Revision: 105790
Author: g.ha
Date: 2015-07-03T18:16:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/TitanCNA/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b627bcb28d18d371156fe30e4a01b041546c4db5

    Corrected CITATIION file

Revision: 105789
Author: bcarvalh
Date: 2015-07-03T16:26:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/oligo/DESCRIPTION
testing git mirror

From: Benilton Carvalho <beniltoncarvalho@gmail.com>
Revision: 105788
Author: z.jia
Date: 2015-07-03T15:22:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/cogena/README.md
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4babc2f20dee3e2bee4ea21c7f551618bf9e3605

    Update README figure title.

Revision: 105787
Author: z.jia
Date: 2015-07-03T15:20:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/cogena/README.md
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f167d5d715146f0530eec85a627270beb7eec7b3

    update README.

Revision: 105786
Author: c.stephan
Date: 2015-07-03T10:09:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/R/simPost.R
simMAE returns pis for all txs in island_id
Revision: 105785
Author: a.cornish
Date: 2015-07-03T08:14:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/SANTA/DESCRIPTION
Modified  /trunk/madman/Rpacks/SANTA/NAMESPACE
Modified  /trunk/madman/Rpacks/SANTA/NEWS
stringr dependency removed
Revision: 105784
Author: a.wachter
Date: 2015-07-03T08:05:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/pwOmics/DESCRIPTION
Modified  /trunk/madman/Rpacks/pwOmics/NAMESPACE
Modified  /trunk/madman/Rpacks/pwOmics/R/pwOmics_consensus_analysis.R
Fix function name problems in pwOmics_consensus_analysis
Revision: 105783
Author: x.zheng
Date: 2015-07-03T07:50:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/R/Conversion.R
Modified  /trunk/madman/Rpacks/SeqArray/R/Methods.R
Modified  /trunk/madman/Rpacks/SeqArray/man/seqAlleleFreq.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqMissing.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqNumAllele.Rd
Modified  /trunk/madman/Rpacks/SeqArray/src/ReadBySample.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/SeqArray.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b25305e822dd24e08dff0c2af26834ab7954040b

    getOption("gds.parallel", FALSE)

Revision: 105782
Author: a.stilp
Date: 2015-07-02T22:56:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GWASTools/R/manhattanPlot.R
Modified  /trunk/madman/Rpacks/GWASTools/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/GWASTools/man/manhattanPlot.Rd
added col= argument to manhattanPlot
Revision: 105781
Author: a.mohamed
Date: 2015-07-02T21:53:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/NetPathMiner/DESCRIPTION
Modified  /trunk/madman/Rpacks/NetPathMiner/R/netWeight.R
added garph depeds for as_graph_nel
Revision: 105779
Author: y.rahmatallah
Date: 2015-07-02T20:51:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSAR/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSAR/data/p53DataSet.rda
Modified  /trunk/madman/Rpacks/GSAR/inst/CITATION
Modified  /trunk/madman/Rpacks/GSAR/inst/NEWS.Rd
commit 2
Revision: 105778
Author: m.love
Date: 2015-07-02T20:48:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
bumping version solely to trigger re-build
Revision: 105777
Author: l.gatto
Date: 2015-07-02T20:06:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/rols/DESCRIPTION
Modified  /trunk/madman/Rpacks/rols/NEWS
Modified  /trunk/madman/Rpacks/rols/tests/testthat/test_queries.R
Merge branch 'master' into local-hedgehog

From: Laurent <lg390@cam.ac.uk>
Revision: 105775
Author: l.goldstein
Date: 2015-07-02T18:28:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/counts.R
Modified  /trunk/madman/Rpacks/SGSeq/R/main.R
Modified  /trunk/madman/Rpacks/SGSeq/man/getSGVariantCounts.Rd
added default argument prefer_junctions = TRUE for calculating variant frequencies
Revision: 105774
Author: p.bellot
Date: 2015-07-02T15:22:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/netbenchmark/R/evaluate.R
- Bugfix in .Adj2Edgelist

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