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Revision: 107063
Author: x.zheng
Date: 2015-08-04T05:44:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/NEWS
Modified  /trunk/madman/Rpacks/gdsfmt/README.md
Modified  /trunk/madman/Rpacks/gdsfmt/man/objdesp.gdsn.Rd
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 22f474ad03bbbf78ae20d01a62274121a1814754

    indicate the location of GDS command-line tools

    * make the behavior of read.gdsn() and readex.gdsn() more similar to R
    x[,] when simplify="auto"
    * fix a typo

Revision: 107062
Author: t.girke
Date: 2015-08-04T04:52:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.R
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9f74252628d25c6b9dde3aeeaae6e1824b125926

    some edits

Revision: 107061
Author: t.girke
Date: 2015-08-04T04:26:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9b4d4c043d4d4278d847d3ec6f5f244517a8532a

    some edits

Revision: 107060
Author: t.girke
Date: 2015-08-04T04:25:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a47de2d8a7635396fc8024979a2a12091edf099b

    some edits

Revision: 107059
Author: t.girke
Date: 2015-08-04T04:19:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9bf9d776c9f0c32142de7fd8cb0b7416b01636db

    some edits

Revision: 107058
Author: t.girke
Date: 2015-08-04T04:19:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 85eb8a0e101a88c9fd9111cdffe8927e5bf08d79

    some edits

Revision: 107057
Author: t.girke
Date: 2015-08-04T04:14:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0da5524463f5f768b8dd01e049d9bf7a2bfc7a5b

    some edits

Revision: 107056
Author: t.girke
Date: 2015-08-04T04:13:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1975e689482274eda7a6001428bdb77a093834bf

    some edits

Revision: 107055
Author: t.girke
Date: 2015-08-04T03:47:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.R
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 20c857bfe146cc5844299d1318edaf1779f7f0d1

    some edits

Revision: 107054
Author: t.girke
Date: 2015-08-04T03:46:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f4a5aede03760c17d3e8477c8145d97ab7de43b2

    some edits

Revision: 107053
Author: t.girke
Date: 2015-08-04T03:40:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 07d1d67d5b2adaa68ab640659358547ae8e8d18a

    some edits

Revision: 107052
Author: t.girke
Date: 2015-08-04T03:39:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 169a095e70a322327c3dfa033cf1c2059c5f6383

    some edits

Revision: 107051
Author: t.girke
Date: 2015-08-04T03:39:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.R
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4287dee21067fc9480df260a190078a32311c1ce

    some edits

Revision: 107050
Author: t.girke
Date: 2015-08-04T03:22:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 746a85fa17fb70d0d1e4608814c86e108e516cce

    some edits

Revision: 107049
Author: t.girke
Date: 2015-08-04T03:16:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.R
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 5211536ea636e49ee8eaaf7c7b573839a6214925

    some edits

Revision: 107048
Author: t.girke
Date: 2015-08-04T03:15:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8bd1cb90b0b2e7e3dd465423b360287aaa7dd48e

    some edits

Revision: 107046
Author: t.girke
Date: 2015-08-04T00:07:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 5dd6c115fd87638c6b5bee02e32aac09ddbd1b68

    some edits

Revision: 107044
Author: t.girke
Date: 2015-08-03T23:27:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 34450dfaf9b2c12733460952d7863e19c662812e

    some edits

Revision: 107042
Author: t.girke
Date: 2015-08-03T23:00:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: aa5d6cdbea4e26bc4c597726e63414d8bac7f371

    some edits

Revision: 107041
Author: t.girke
Date: 2015-08-03T22:52:14+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.R
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8badd8dffd52a3a3c0ba453d14f0a481e9e1e057

    some edits

Revision: 107040
Author: t.girke
Date: 2015-08-03T22:25:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 24d872f3e55bc6f13c14ba18878cefaf0d718c1b

    some edits

Revision: 107039
Author: stvjc
Date: 2015-08-03T22:18:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/gwascat/man/gwcex2gviz.Rd
minor change in example, need right dataset
Revision: 107038
Author: v.obenchain
Date: 2015-08-03T22:01:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/coordinate-mapping-methods.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_coordinate-mapping-methods.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/coordinate-mapping-methods.Rd
coordinate mapping:

- add pmapToTranscripts,Ranges,GRangesList and
  pmapFromTranscripts,Ranges,GRangesList methods
- name matching in mapFromTranscripts() is now done with
  seqnames(x) and names(transcripts)
- support recycling when length(transcripts) == 1 for p* functions
Revision: 107037
Author: stvjc
Date: 2015-08-03T21:44:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/gwascat/DESCRIPTION
Added  /trunk/madman/Rpacks/gwascat/vignettes/gwascatOnt.Rmd
new vignette emphasizing ontology graph
Revision: 107034
Author: m.teng
Date: 2015-08-03T21:28:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/rnaseqcomp/inst/CITATION
Modified  /trunk/madman/Rpacks/rnaseqcomp/vignettes/rnaseqcomp.bib
citation updated
Revision: 107033
Author: l.zhu
Date: 2015-08-03T21:25:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/T2.fa
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/T2plus100OffTargets.bed
Added  /trunk/madman/Rpacks/CRISPRseek/man/offTargetAnalysisOfPeakRegions.Rd
Add documentation to offTargetAnalysisOfPeakRegions and export the function
Revision: 107032
Author: l.zhu
Date: 2015-08-03T21:24:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/NAMESPACE
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysisOfPeakRegions.R
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/CITATION
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/NEWS
Add documentation to offTargetAnalysisOfPeakRegions and export the function
Revision: 107029
Author: s.aibar
Date: 2015-08-03T21:05:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/geNetClassifier/DESCRIPTION
Modified  /trunk/madman/Rpacks/geNetClassifier/NEWS
Modified  /trunk/madman/Rpacks/geNetClassifier/R/functions.public.R
1.9.3 Compatibility with igraph 1.0
Revision: 107028
Author: t.girke
Date: 2015-08-03T20:59:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 07283018a9d193596629456ea0ce41fd821a4175

    some edits

Revision: 107027
Author: t.girke
Date: 2015-08-03T20:34:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f40e46152ab21edd109fd65a86a82b468a7163f7

    some edits

Revision: 107026
Author: t.girke
Date: 2015-08-03T20:34:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1e7f7100e152ecfccba303f0ecbd9bb38a6d19b1

    some edits

Revision: 107025
Author: t.girke
Date: 2015-08-03T20:11:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 12ca928f46461d6f8920490017b9a89711aa5c0d

    some edits

Revision: 107024
Author: m.teng
Date: 2015-08-03T19:36:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/rnaseqcomp/DESCRIPTION
Modified  /trunk/madman/Rpacks/rnaseqcomp/inst/CITATION
Modified  /trunk/madman/Rpacks/rnaseqcomp/inst/NEWS
Modified  /trunk/madman/Rpacks/rnaseqcomp/vignettes/rnaseqcomp.bib
citation update
Revision: 107022
Author: t.girke
Date: 2015-08-03T19:07:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/tophat.param
Commit made by the Bioconductor Git-SVN bridge.

Commit id: d7c2281dd9ab94f17e4ee1d09c45fb9c42de60e6

    some edits

Revision: 107021
Author: t.girke
Date: 2015-08-03T18:48:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 24f6d770fcf7ed38e29ac689ed7e54c836f85605

    some edits

Revision: 107020
Author: t.girke
Date: 2015-08-03T18:45:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1e8a5ae9b551f0061553db60a2695215614b7749

    some edits

Revision: 107019
Author: t.girke
Date: 2015-08-03T18:31:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/README.md
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b5b4e437bfc704b96a853206e070ff8ae28c8203

    some edits

Revision: 107018
Author: t.girke
Date: 2015-08-03T18:27:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 5a3d6960b375cd740845c7207c3a42ec89313a52

    some edits

Revision: 107017
Author: t.girke
Date: 2015-08-03T18:18:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2453cbbf06f13cc9a9833929fdc87333f362b606

    some edits

Revision: 107016
Author: t.girke
Date: 2015-08-03T18:18:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 5d634a69445bc79adb8087e77953105e1e65c37c

    some edits

Revision: 107015
Author: t.girke
Date: 2015-08-03T18:16:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 65e6fa480f8f5915362b2cdd28159696131dd7d1

    some edits

Revision: 107014
Author: t.girke
Date: 2015-08-03T18:13:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/README.md
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4368ea39fed560c6217da4dacc46c8128d9c7753

    some edits

Revision: 107012
Author: t.girke
Date: 2015-08-03T18:02:00+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/bibtex.bib
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/images
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/images/SystemPipeR_Workflow.png
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/logo.png
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.Rmd
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides.html
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/__packages
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/setup_81cb88a5f78567518def92abecd81c4d.RData
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/setup_81cb88a5f78567518def92abecd81c4d.rdb
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/setup_81cb88a5f78567518def92abecd81c4d.rdx
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/targetsSE_a03ec1a532a8b8253801a4b1ab5b7c88.RData
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/targetsSE_a03ec1a532a8b8253801a4b1ab5b7c88.rdb
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/slides/systemPipeRslides_cache/html/targetsSE_a03ec1a532a8b8253801a4b1ab5b7c88.rdx
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a633c2c4da7da185e8f7d83d757ab1b94b08cba6

    some edits

Revision: 107011
Author: stvjc
Date: 2015-08-03T17:36:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/gwascat/man/gwastagger.Rd
fix gwastagger man page example
Revision: 107009
Author: stvjc
Date: 2015-08-03T16:48:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/gwascat/DESCRIPTION
Modified  /trunk/madman/Rpacks/gwascat/NEWS
Modified  /trunk/madman/Rpacks/gwascat/R/obotools.R
Modified  /trunk/madman/Rpacks/gwascat/data/ebicat37.rda
Modified  /trunk/madman/Rpacks/gwascat/data/ebicat38.rda
minor enhancement to obo2graphNEL to deal with trailing blank, updated content
Revision: 107008
Author: n.sidiropoulos
Date: 2015-08-03T16:00:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/RNAprobR/R/bedgraph2norm.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 425eb73cb584ec4f59bae8518148eaf776bc577d

    Removed "" from "FALSE"

Revision: 107007
Author: n.sidiropoulos
Date: 2015-08-03T15:34:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/RNAprobR/R/bed_to_TranscriptDb.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e7b7a0cbfc1431155de546131a0f259e118dbd95

    Restored changes.

Revision: 107006
Author: n.sidiropoulos
Date: 2015-08-03T15:29:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/RNAprobR/DESCRIPTION
Modified  /trunk/madman/Rpacks/RNAprobR/NEWS
Modified  /trunk/madman/Rpacks/RNAprobR/R/bed_to_TranscriptDb.R
Modified  /trunk/madman/Rpacks/RNAprobR/R/bedgraph2norm.R
Added  /trunk/madman/Rpacks/RNAprobR/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9718c82aa3341bf7365397da18776255272ce622

    Merge branch 'master' of https://github.com/sidiropoulos/RNAprobR


Commit id: aadf987712021158a0ac6970046b0716ffad8287

    Added citation file.


Commit id: f2ed5a0ba1a3641f21554020b3e2bd70d53f2a36

    Fixed critical error where the default ignore.strand = "TRUE" produced erroneous results.


Commit id: 47a01e3a992c42d6dbab1e3445a2ef1fc8a1b9d2

    Version updates


Commit id: 2a5f655ee69a7057867a283e0f06d787123d9cf9

    Version update. Added date.

Revision: 107005
Author: n.leng
Date: 2015-08-03T14:31:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBSeq/R/EBMultiTest.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7d57e26d7d31126206c82f958705ec8754b7c005

    Update EBMultiTest.R

Revision: 107004
Author: n.leng
Date: 2015-08-03T14:30:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBSeq/R/EBTest.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: ecf9c3613db24de73253942978b484a7f99fbe58

    Update EBTest.R

Revision: 107003
Author: d.rossell
Date: 2015-08-03T14:23:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/src/cstat.cpp
Fixed bug in cholS_inv (no effect)
Revision: 107002
Author: l.zhu
Date: 2015-08-03T14:06:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysisOfPeakRegions.R
fixed build bug
Revision: 107001
Author: p.angerer
Date: 2015-08-03T13:51:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/DESCRIPTION
bumped version to 0.99.15
Revision: 107000
Author: f.schmich
Date: 2015-08-03T13:40:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/gespeR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2ab223989dc3e9199997818ffecdb4f73d02c4bc

    version bump

Revision: 106999
Author: f.schmich
Date: 2015-08-03T13:40:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/gespeR/R/Phenotypes-class.R
Modified  /trunk/madman/Rpacks/gespeR/R/gespeR-class.R
Modified  /trunk/madman/Rpacks/gespeR/R/gespeR-functions.R
Modified  /trunk/madman/Rpacks/gespeR/R/gespeR-generics.R
Modified  /trunk/madman/Rpacks/gespeR/R/gespeR-methods.R
Modified  /trunk/madman/Rpacks/gespeR/data/stabilityfits.RData
Added  /trunk/madman/Rpacks/gespeR/man/dim-Phenotypes-method.Rd
Modified  /trunk/madman/Rpacks/gespeR/man/plot.Phenotypes.Rd
Modified  /trunk/madman/Rpacks/gespeR/man/values-methods.Rd
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR-concordance.tex
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR.Rnw
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR.log
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR.pdf
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR.synctex.gz
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR.tex
Modified  /trunk/madman/Rpacks/gespeR/vignettes/gespeR.toc
Modified  /trunk/madman/Rpacks/gespeR/vignettes/tmp/gespeR-plot_concordance-1.pdf
Modified  /trunk/madman/Rpacks/gespeR/vignettes/tmp/gespeR-plot_concordance-2.pdf
Modified  /trunk/madman/Rpacks/gespeR/vignettes/tmp/gespeR-plot_cv-1.pdf
Modified  /trunk/madman/Rpacks/gespeR/vignettes/tmp/gespeR-plot_phenotypes-1.pdf
Deleted  /trunk/madman/Rpacks/gespeR/vignettes/tmp/gespeR-plot_stability-1.pdf
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a31ec13e6c911367be0650bd7a507f1630cc0a48

    clean CHECK

Revision: 106998
Author: d.schmolze
Date: 2015-08-03T13:16:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/EMDomics/R/EMD.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 51cf5c62b8088e4c0f4d3662937e82ff06fd1ecf

    Fixed NA problem

Revision: 106995
Author: d.gatti
Date: 2015-08-03T10:30:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOQTL/R/condense.model.probs.R
Added  /trunk/madman/Rpacks/DOQTL/R/scanone.assoc.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4715b614abb947b623e43e0dd0a89730b3438040

    Added get.diplotypetohaplotype.matrix and scanone.assoc

Revision: 106993
Author: j.gehring
Date: 2015-08-03T09:30:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/SomaticSignatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/SomaticSignatures/vignettes/SomaticSignatures-vignette.Rhtml
Modified  /trunk/madman/Rpacks/SomaticSignatures/vignettes/SomaticSignatures-vignette.org
Commit made by the Bioconductor Git-SVN bridge.

Commit id: dcb722c2cb45c5224aefbe2514f499b7379eb735

    2.5.6: Fix DOI link and reformat citation

Revision: 106992
Author: d.low
Date: 2015-08-03T07:31:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/deltaGseg/DESCRIPTION
update

From: d.low <lowdiana@gmail.com>
Revision: 106991
Author: d.low
Date: 2015-08-03T07:16:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/deltaGseg/DESCRIPTION
Modified  /trunk/madman/Rpacks/deltaGseg/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/deltaGseg/inst/NEWS
Merge branch 'master' into devel

* master:
  r
  update test
  update
  update
  update
  fixed date
  fixed date
  update changepoint functions
  Creating branch for BioC 3.1 release.

Conflicts:
	DESCRIPTION

From: d.low <lowdiana@gmail.com>
Revision: 106990
Author: d.low
Date: 2015-08-03T07:16:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/deltaGseg/DESCRIPTION
v

From: d.low <lowdiana@gmail.com>
Revision: 106982
Author: t.girke
Date: 2015-08-03T03:20:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/README
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: da75936422a55f7817f1b28040e6adf950afff13

    vignette updates

Revision: 106981
Author: d.tenenbaum
Date: 2015-08-03T00:04:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
bump version to appropriate number (y of x.y.z must be odd in devel)
Revision: 106977
Author: z.gu
Date: 2015-08-01T18:51:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-HeatmapAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-SingleAnnotation-method.rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 722ae931d95ad2242857b94a1383ad39650a6012

    refresh documentations

Revision: 106976
Author: z.gu
Date: 2015-08-01T17:25:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/HeatmapAnnotation-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/HeatmapList-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/SingleAnnotation-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/annotation_fun.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/ComplexHeatmap.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 412fce42e41a87c7be53141c33f5d08beedbb27a

    optimized axis in annotations

Revision: 106975
Author: f.commo
Date: 2015-08-01T16:35:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/rCGH/DESCRIPTION
Modified  /trunk/madman/Rpacks/rCGH/NEWS
Modified  /trunk/madman/Rpacks/rCGH/R/AllClasses.R
Modified  /trunk/madman/Rpacks/rCGH/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/rCGH/R/AllHelperFunctions.R
Modified  /trunk/madman/Rpacks/rCGH/R/AllMethods.R
Modified  /trunk/madman/Rpacks/rCGH/R/plotFunctions.R
Modified  /trunk/madman/Rpacks/rCGH/inst/shinyProfile/helpers.R
Modified  /trunk/madman/Rpacks/rCGH/inst/shinyProfile/server.R
Modified  /trunk/madman/Rpacks/rCGH/inst/shinyProfile/ui.R
Modified  /trunk/madman/Rpacks/rCGH/inst/unitTests/test_rCGH.R
Modified  /trunk/madman/Rpacks/rCGH/man/AllAccessors.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/byGeneTable.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/multiplot.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/plotProfile.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/rCGH-Agilent-class.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/rCGH-SNP6-class.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/rCGH-class.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/rCGH-cytoScan-class.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/rCGH-package.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/readAffyCytoScan.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/readAffySNP6.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/readAgilent.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/segmentCGH.Rd
Modified  /trunk/madman/Rpacks/rCGH/man/view.Rd
Modified  /trunk/madman/Rpacks/rCGH/vignettes/rCGH.Rnw
Modified  /trunk/madman/Rpacks/rCGH/vignettes/view.png
v0.99.7
Revision: 106974
Author: bolstad
Date: 2015-08-01T16:22:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/affyio/DESCRIPTION
version number needs to be odd for devel
Revision: 106973
Author: m.lawrence
Date: 2015-08-01T15:59:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/R/bigWig.R
drop seqlevels from 'which' that do not exist in BigWig file, with
warning (instead of an error)
Revision: 106972
Author: m.lawrence
Date: 2015-08-01T15:51:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Modified  /trunk/madman/Rpacks/rtracklayer/R/gff.R
Added  /trunk/madman/Rpacks/rtracklayer/R/ncbi.R
Modified  /trunk/madman/Rpacks/rtracklayer/R/ranges.R
retrieve organism info from NCBI via GFF3 ##species directive
(experimental), should be useful for GenomicFeatures::makeTxDbFromGFF
Revision: 106970
Author: g.yu
Date: 2015-08-01T13:22:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/README.md
Modified  /trunk/madman/Rpacks/ggtree/vignettes/ggtree.Rmd
add doc
Revision: 106967
Author: m.schroeder
Date: 2015-08-01T10:12:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/genefu/DESCRIPTION
Modified  /trunk/madman/Rpacks/genefu/NAMESPACE
Modified  /trunk/madman/Rpacks/genefu/R/endoPredict.R
Modified  /trunk/madman/Rpacks/genefu/R/gene70.R
Modified  /trunk/madman/Rpacks/genefu/R/gene76.R
Modified  /trunk/madman/Rpacks/genefu/R/genius.R
Modified  /trunk/madman/Rpacks/genefu/R/ggi.R
Added  /trunk/madman/Rpacks/genefu/R/molecular.subtyping.R
Modified  /trunk/madman/Rpacks/genefu/R/oncotypedx.R
Modified  /trunk/madman/Rpacks/genefu/R/ovcAngiogenic.R
Modified  /trunk/madman/Rpacks/genefu/R/ovcCrijns.R
Modified  /trunk/madman/Rpacks/genefu/R/ovcTCGA.R
Modified  /trunk/madman/Rpacks/genefu/R/ovcYoshihara.R
Modified  /trunk/madman/Rpacks/genefu/R/pik3cags.R
Modified  /trunk/madman/Rpacks/genefu/R/power.cor.R
Modified  /trunk/madman/Rpacks/genefu/R/rorS.R
Modified  /trunk/madman/Rpacks/genefu/R/subtype.cluster.R
Modified  /trunk/madman/Rpacks/genefu/R/subtype.cluster.predict.R
Modified  /trunk/madman/Rpacks/genefu/R/tamr13.R
Modified  /trunk/madman/Rpacks/genefu/README
Modified  /trunk/madman/Rpacks/genefu/data/expos.rda
Modified  /trunk/madman/Rpacks/genefu/data/mod1.rda
Modified  /trunk/madman/Rpacks/genefu/data/mod2.rda
Modified  /trunk/madman/Rpacks/genefu/data/modelOvcAngiogenic.rda
Modified  /trunk/madman/Rpacks/genefu/data/nkis.rda
Modified  /trunk/madman/Rpacks/genefu/data/pam50.rda
Modified  /trunk/madman/Rpacks/genefu/data/pam50.robust.rda
Modified  /trunk/madman/Rpacks/genefu/data/pam50.scale.rda
Modified  /trunk/madman/Rpacks/genefu/data/scmgene.robust.rda
Modified  /trunk/madman/Rpacks/genefu/data/scmod1.robust.rda
Modified  /trunk/madman/Rpacks/genefu/data/scmod2.robust.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.endoPredict.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.gene70.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.gene76.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.genius.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.ggi.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.oncotypedx.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.pik3cags.rda
Modified  /trunk/madman/Rpacks/genefu/data/sig.tamr13.rda
Modified  /trunk/madman/Rpacks/genefu/data/sigOvcAngiogenic.rda
Modified  /trunk/madman/Rpacks/genefu/data/sigOvcCrijns.rda
Modified  /trunk/madman/Rpacks/genefu/data/sigOvcSpentzos.rda
Modified  /trunk/madman/Rpacks/genefu/data/sigOvcTCGA.rda
Modified  /trunk/madman/Rpacks/genefu/data/sigOvcYoshihara.rda
Modified  /trunk/madman/Rpacks/genefu/data/ssp2003.rda
Modified  /trunk/madman/Rpacks/genefu/data/ssp2003.robust.rda
Modified  /trunk/madman/Rpacks/genefu/data/ssp2003.scale.rda
Modified  /trunk/madman/Rpacks/genefu/data/ssp2006.rda
Modified  /trunk/madman/Rpacks/genefu/data/ssp2006.robust.rda
Modified  /trunk/madman/Rpacks/genefu/data/ssp2006.scale.rda
Modified  /trunk/madman/Rpacks/genefu/data/vdxs.rda
Modified  /trunk/madman/Rpacks/genefu/man/expos.Rd
Modified  /trunk/madman/Rpacks/genefu/man/fuzzy.ttest.Rd
Modified  /trunk/madman/Rpacks/genefu/man/genefu-package.Rd
Modified  /trunk/madman/Rpacks/genefu/man/map.datasets.Rd
Added  /trunk/madman/Rpacks/genefu/man/molecular.subtyping.Rd
Modified  /trunk/madman/Rpacks/genefu/man/nkis.Rd
Modified  /trunk/madman/Rpacks/genefu/man/ovcAngiogenic.Rd
Modified  /trunk/madman/Rpacks/genefu/man/ovcCrijns.Rd
Modified  /trunk/madman/Rpacks/genefu/man/ovcTCGA.Rd
Modified  /trunk/madman/Rpacks/genefu/man/ovcYoshihara.Rd
Modified  /trunk/madman/Rpacks/genefu/man/rorS.Rd
Modified  /trunk/madman/Rpacks/genefu/man/setcolclass.df.Rd
Modified  /trunk/madman/Rpacks/genefu/man/sig.gene70.Rd
Modified  /trunk/madman/Rpacks/genefu/vignettes/genefu.Rnw
Included new molecular subtyping function, new vignette and minor fixes. Version bump to 2.0.2.
Revision: 106966
Author: g.yu
Date: 2015-08-01T09:16:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/README.md
Modified  /trunk/madman/Rpacks/ggtree/vignettes/ggtree.Rmd
add external doc

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