Subversion Logs

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

This list is also available as an RSS feed. (release branch)

Revision: 94344
Author: khansen
Date: 2014-09-21T17:07:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/minfi/man/preprocessNoob.Rd
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 58aa3c7604410bea28d77c61f4938ab56eab2254

    Fixed a man page issues; add GitHub URL

Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-21 13:07:30 -0400
Author date: 2014-09-21 13:07:30 -0400
Revision: 94343
Author: khansen
Date: 2014-09-21T17:05:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/bsseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/bsseq/inst/NEWS.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 970b9726dd0d9bb72a11a3e4fc3308a9da3569ab

    added GitHub url to DESCRIPTION

Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-21 13:05:37 -0400
Author date: 2014-09-21 13:05:37 -0400
Revision: 94342
Author: khansen
Date: 2014-09-21T16:45:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/bsseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/bsseq/R/BSseq_class.R
Modified  /trunk/madman/Rpacks/bsseq/man/hasGRanges-class.Rd
Modified  /trunk/madman/Rpacks/bsseq/inst/CITATION
Modified  /trunk/madman/Rpacks/bsseq/inst/NEWS.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 64613833bc6c16668d484639dc935ea5d721ec28

    fixed various small issues like man pages, CITATION etc.

Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-21 12:44:59 -0400
Author date: 2014-09-21 12:44:59 -0400
Revision: 94341
Author: sdavis2
Date: 2014-09-21T15:39:05+00:00
Paths:
Deleted  /trunk/madman/Rpacks/GEOquery/vignettes/GEOquery.Rnw
Added  /trunk/madman/Rpacks/GEOquery/vignettes/.gitignore
Modified  /trunk/madman/Rpacks/GEOquery/DESCRIPTION
Added  /trunk/madman/Rpacks/GEOquery/vignettes/GEOquery.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 5f32d12591417c6da356f1088ce11a1936697e6f

    Merge branch 'HTMLVignette'

Committed by: Sean Davis
Author Name: Sean Davis
Commit date: 2014-09-21 11:38:27 -0400
Author date: 2014-09-21 11:38:27 -0400

Commit id: d95ed5e16b01fda2c616764bd33f1200e7a448ad

    Convert vignette to rmarkdown and HTML

Committed by: Sean Davis
Author Name: Sean Davis
Commit date: 2014-09-21 11:37:01 -0400
Author date: 2014-09-21 11:37:01 -0400
Revision: 94340
Author: khansen
Date: 2014-09-21T15:03:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/illuminaio/vignettes/illuminaio.Rnw
Added  /trunk/madman/Rpacks/illuminaio/vignettes/illuminaio.bib
Modified  /trunk/madman/Rpacks/illuminaio/inst/CITATION
Modified  /trunk/madman/Rpacks/illuminaio/inst/NEWS
added citation to vignette, cleaned up vignette
Revision: 94339
Author: khansen
Date: 2014-09-21T14:48:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/illuminaio/vignettes/illuminaio.Rnw
Modified  /trunk/madman/Rpacks/illuminaio/DESCRIPTION
Modified  /trunk/madman/Rpacks/illuminaio/inst/CITATION
Modified  /trunk/madman/Rpacks/illuminaio/inst/NEWS
fixed vignette error; updated CITATION
Revision: 94338
Author: rscharpf
Date: 2014-09-21T14:38:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c330bfd25d19c6022320af578c63d31be7cbb446

    Add ArrayTV to suggests

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-21 10:37:55 -0400
Author date: 2014-09-21 10:37:55 -0400
Revision: 94337
Author: sdavis2
Date: 2014-09-21T14:13:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.gitignore
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c6a9d9454aa0898d9c0dd0b2e418c388619520f0

    Added .Rhistory to .gitignore

Committed by: Sean Davis
Author Name: Sean Davis
Commit date: 2014-09-21 10:13:23 -0400
Author date: 2014-09-21 10:13:23 -0400
Revision: 94336
Author: sdavis2
Date: 2014-09-21T14:04:56+00:00
Paths:
Added  /trunk/madman/Rpacks/GEOquery/.Rbuildignore
Modified  /trunk/madman/Rpacks/GEOquery/.gitignore
Added  /trunk/madman/Rpacks/GEOquery/GEOquery.Rproj
setting up git-svn bridge
Revision: 94335
Author: m.alvarez
Date: 2014-09-20T23:42:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/viper/R/viper.r
=Modification in viperSignature method that improves stability for small datasets
Revision: 94334
Author: m.castro
Date: 2014-09-20T22:26:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/RTN/NAMESPACE
Modified  /trunk/madman/Rpacks/RTN/R/TNI-methods.R
Modified  /trunk/madman/Rpacks/RTN/DESCRIPTION
Modified  /trunk/madman/Rpacks/RTN/R/AllSupplementsTNI.R
updated tni methods
Revision: 94333
Author: m.castro
Date: 2014-09-20T22:22:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/RedeR/R/Supplements.R
Modified  /trunk/madman/Rpacks/RedeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/RedeR/inst/java/reder.jar
update interface
Revision: 94332
Author: x.zheng
Date: 2014-09-20T21:59:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPRelate/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 3896970079d4696ad7dd57c606cb6de4747d1d36

    Update README.md

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-09-20 16:59:45 -0500
Author date: 2014-09-20 16:59:45 -0500
Revision: 94331
Author: x.zheng
Date: 2014-09-20T21:50:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPRelate/DESCRIPTION
Modified  /trunk/madman/Rpacks/SNPRelate/R/AllUtilities.R
Modified  /trunk/madman/Rpacks/SNPRelate/src/R_SNPRelate.c
Added  /trunk/madman/Rpacks/SNPRelate/src/R_GDS_Patch.h
Modified  /trunk/madman/Rpacks/SNPRelate/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 38b68336624ed77b2a809a5471bcd2d4d2ceea80

    SNPRelate_0.99.2

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-09-20 16:50:14 -0500
Author date: 2014-09-20 16:50:14 -0500
Revision: 94326
Author: mtmorgan
Date: 2014-09-20T19:19:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/codetoolsBioC/R/findExternalDeps.R
Modified  /trunk/madman/Rpacks/codetoolsBioC/DESCRIPTION
allow exported S4 methods to find their imported generics
Revision: 94324
Author: mtmorgan
Date: 2014-09-20T17:32:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
version bump (nearly forgot!)
Revision: 94323
Author: mtmorgan
Date: 2014-09-20T17:25:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/vignettes/HtmlStyle.Rmd
re-organize html vignette

- '...' args can be passed to paste() without do.call
- rmarkdown is now on CRAN
- illustrate inclusion of VignetteEngine command w/ code
- move RStudio-specific material to end of document
- minor markup additions, e.g., italicize software (RStudio, R,
  Bioconductor)
- wrap lines to 80 characters
- include sessionInfo() to model good behavior
Revision: 94322
Author: mtmorgan
Date: 2014-09-20T17:21:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/R/markdown.R
code 'clean-up'

- avoid long lines and excessive nesting of commands
- use '<-' rather than '=', to provide a good example
Revision: 94321
Author: mtmorgan
Date: 2014-09-20T17:20:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/vignettes/LatexStyle.Rnw
consistent latex / html vignette structure
Revision: 94320
Author: d.henderson
Date: 2014-09-20T06:24:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/src/sortped.cc
remove ancestor variable
Revision: 94319
Author: d.henderson
Date: 2014-09-20T06:21:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/man/TDT.Rd
remove superfluous }
Revision: 94318
Author: p.shannon
Date: 2014-09-20T00:37:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/ui.R
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/server.R
the "Find Interactions" button is enabled only when a provider is present, and gene name of >= 2 characters
has been entered.
Revision: 94316
Author: m.carlson
Date: 2014-09-19T23:37:02+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/man/run_edgeR.Rd
Added  /trunk/madman/Rpacks/GOsummaries/man/metabolomic_example.Rd
Added  /trunk/madman/Rpacks/seqplots/man/PlotSetList-class.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/forward_enabled.png
Added  /trunk/madman/Rpacks/GOsummaries/vignettes/GS.pdf
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/10_00.png
Added  /trunk/madman/Rpacks/systemPipeR/man/sysargs.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/upload.html
Added  /trunk/madman/Rpacks/systemPipeR/man/systemArgs.Rd
Added  /trunk/madman/Rpacks/GOsummaries/data
Added  /trunk/madman/Rpacks/GOsummaries/vignettes/GOsummaries-basics.Rnw
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_04.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/fnPlotHeatmap.R
Added  /trunk/madman/Rpacks/seqplots/R/int_imPlot2.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/marked.min.js
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/font/fontawesome-webfont.ttf
Added  /trunk/madman/Rpacks/TSCAN/R/orderscore.R
Added  /trunk/madman/Rpacks/seqplots/man/getPlotSetArray.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/font/fontawesome-webfont.svg
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images
Added  /trunk/madman/Rpacks/GOsummaries/man/gosummaries.kmeans.Rd
Added  /trunk/madman/Rpacks/geecc/R/concub-class.R
Added  /trunk/madman/Rpacks/geecc/inst
Added  /trunk/madman/Rpacks/rain/R/calcStatistic.R
Added  /trunk/madman/Rpacks/geecc/data/datalist
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/spacelab.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js
Added  /trunk/madman/Rpacks/TSCAN/data/datalist
Added  /trunk/madman/Rpacks/GOsummaries/README.md
Added  /trunk/madman/Rpacks/TSCAN/R/singlegeneplot.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/jquery.min.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img
Added  /trunk/madman/Rpacks/seqplots/inst/extdata/GSM1208360_chrI_100Kb_q5_sample.bw
Added  /trunk/madman/Rpacks/GOsummaries/man/customize.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/server_config.R
Added  /trunk/madman/Rpacks/seqplots/vignettes/QuickStart.Rmd
Added  /trunk/madman/Rpacks/TSCAN/vignettes/TSCAN.Rnw
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_01.png
Added  /trunk/madman/Rpacks/GOsummaries/man/GOsummaries-package.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js
Added  /trunk/madman/Rpacks/systemPipeR/inst
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/color/arrow.gif
Added  /trunk/madman/Rpacks/seqplots/man/PlotSetPair-class.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_02.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_06.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/ico_noax.png
Added  /trunk/madman/Rpacks/systemPipeR/man/returnRPKM.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/js_addons.js
Added  /trunk/madman/Rpacks/TSCAN/man
Added  /trunk/madman/Rpacks/systemPipeR/R/geneSetAnalysis.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/DataTables/DT_bootstrap.js
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/ui.R
Added  /trunk/madman/Rpacks/systemPipeR/vignettes
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/NewFont.woff
Added  /trunk/madman/Rpacks/GOsummaries/man/tissue_example.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/jquery.ba-throttle-debounce.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_04.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/jquery-ui.min.js
Added  /trunk/madman/Rpacks/seqplots/R/PlotSetArray-class.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_08.png
Added  /trunk/madman/Rpacks/TSCAN
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/sort_both.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/afterHTMLgridrender.js
Added  /trunk/madman/Rpacks/TSCAN/man/preprocess.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/TableTools.css
Added  /trunk/madman/Rpacks/systemPipeR/man/alignStats.Rd
Added  /trunk/madman/Rpacks/GOsummaries/man/metagenomic_example.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui/loadModal.html
Added  /trunk/madman/Rpacks/seqplots/R/MotifSetup-class.R
Added  /trunk/madman/Rpacks/GOsummaries/data/gs_kmeans.rda
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeChIPseq.Rnw
Added  /trunk/madman/Rpacks/seqplots/inst/extdata/GSM1208361_chrI_100Kb_PeakCalls.bed
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_02.png
Added  /trunk/madman/Rpacks/rain
Added  /trunk/madman/Rpacks/geecc/DESCRIPTION
Added  /trunk/madman/Rpacks/rain/man/rain-package.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_01.png
Added  /trunk/madman/Rpacks/geecc/man/plotConCub.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/extdata/precalc_plotset.Rdata
Added  /trunk/madman/Rpacks/GOsummaries/R/wordcloud.r
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/color/cross.gif
Added  /trunk/madman/Rpacks/seqplots/inst/extdata/Transcripts_ce10_chrI_100Kb.bed
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_02.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/jquery.cookie.js
Added  /trunk/madman/Rpacks/geecc/R/zzz.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/css/jquery.fileupload-ui.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_03.png
Added  /trunk/madman/Rpacks/seqplots/man/plotHeatmap.Rd
Added  /trunk/madman/Rpacks/geecc/R
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/bowtiePE.param
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/cors/jquery.postmessage-transport.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/sort_asc_disabled.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/cerulean.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/tmpl.min.js
Added  /trunk/madman/Rpacks/seqplots/R
Added  /trunk/madman/Rpacks/seqplots/R/run.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/back_enabled.png
Added  /trunk/madman/Rpacks/geecc/vignettes/geecc.bib
Added  /trunk/madman/Rpacks/TSCAN/vignettes
Added  /trunk/madman/Rpacks/rain/inst/NEWS
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/slate.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/img
Added  /trunk/madman/Rpacks/GOsummaries/man/gosummaries.MArrayLM.Rd
Added  /trunk/madman/Rpacks/seqplots/R/plotHeatmap.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/DataTables/DT_filter.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/10_01.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/README.md
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/DEGcounts.pdf
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/global.R
Added  /trunk/madman/Rpacks/GOsummaries/data/metagenomic_example.RData
Added  /trunk/madman/Rpacks/geecc/NAMESPACE
Added  /trunk/madman/Rpacks/seqplots/man/seqplots.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_01.png
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/heatmap1.pdf
Added  /trunk/madman/Rpacks/rain/inst
Added  /trunk/madman/Rpacks/seqplots/NAMESPACE
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL/server_plotHeatmap.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_05.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/DT_bootstrap.css
Added  /trunk/madman/Rpacks/geecc/man/GO2list.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/jquery.fileupload-ui.js
Added  /trunk/madman/Rpacks/GOsummaries/data/gs_limma_exp.rda
Added  /trunk/madman/Rpacks/GOsummaries/man/panel_boxplot.Rd
Added  /trunk/madman/Rpacks/geecc/man/marioni.Rd
Added  /trunk/madman/Rpacks/geecc/man/runConCub.Rd
Added  /trunk/madman/Rpacks/rain/R/mainFunction.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/plotMext.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/fnProcSequenceFeatures.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/color/jscolor.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/simplex.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_02.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/DataTables/jquery.dataTables.js
Added  /trunk/madman/Rpacks/TSCAN/vignettes/TSCAN-concordance.tex
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_03.png
Added  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Added  /trunk/madman/Rpacks/GOsummaries/man/add_expression.gosummaries.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/mask2.png
Added  /trunk/madman/Rpacks/geecc/R/geecc.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui.R
Added  /trunk/madman/Rpacks/TSCAN/R/TSCANui.R
Added  /trunk/madman/Rpacks/systemPipeR/README.md
Added  /trunk/madman/Rpacks/geecc/man
Added  /trunk/madman/Rpacks/TSCAN/data
Added  /trunk/madman/Rpacks/TSCAN/R/TSCAN.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/font/fontawesome-webfont.woff
Added  /trunk/madman/Rpacks/seqplots/man/PlotSetArray-class.Rd
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rnw
Added  /trunk/madman/Rpacks/GOsummaries/NAMESPACE
Added  /trunk/madman/Rpacks/systemPipeR/man/getQsubargs.Rd
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/www/style.css
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/SRR446027_1.fastq
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/SRR446029_1.fastq
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_01.png
Added  /trunk/madman/Rpacks/systemPipeR/R/utilities.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/cyborg.min.css
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/tophat.param
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/color
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/color/hv.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_05.png
Added  /trunk/madman/Rpacks/rain/man
Added  /trunk/madman/Rpacks/GOsummaries/NEWS
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/server.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_09.png
Added  /trunk/madman/Rpacks/GOsummaries/data/datalist
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions
Added  /trunk/madman/Rpacks/seqplots
Added  /trunk/madman/Rpacks/seqplots/R/seqplots-package.R
Added  /trunk/madman/Rpacks/TSCAN/R/difftest.R
Added  /trunk/madman/Rpacks/seqplots/inst/extdata
Added  /trunk/madman/Rpacks/seqplots/vignettes/SeqPlotsGUI.Rmd
Added  /trunk/madman/Rpacks/GOsummaries/src
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/back_enabled_hover.png
Added  /trunk/madman/Rpacks/systemPipeR/man/catDB-class.Rd
Added  /trunk/madman/Rpacks/rain/NAMESPACE
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/SRR446030_1.fastq
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_03.png
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/test_classes.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_10.png
Added  /trunk/madman/Rpacks/seqplots/man/plotAverage.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_03.png
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/www
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/sample_tree.pdf
Added  /trunk/madman/Rpacks/seqplots/man/plotMext.Rd
Added  /trunk/madman/Rpacks/geecc/man/concubfilter-class.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_04.png
Added  /trunk/madman/Rpacks/systemPipeR/R/developerFct.R
Added  /trunk/madman/Rpacks/GOsummaries/man/gosummaries.matrix.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/font/FontAwesome.otf
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_05_06.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL/server_plotLineplot.R
Added  /trunk/madman/Rpacks/geecc/data
Added  /trunk/madman/Rpacks/GOsummaries/R/exampleDatasets.r
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/targets.txt
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/main.js
Added  /trunk/madman/Rpacks/TSCAN/R/plotpseudotime.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/bootstrap.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/font-awesome.min.css
Added  /trunk/madman/Rpacks/seqplots/man/MotifSetup-class.Rd
Added  /trunk/madman/Rpacks/systemPipeR/man
Added  /trunk/madman/Rpacks/seqplots/R/int_plotMext.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_02.png
Added  /trunk/madman/Rpacks/GOsummaries/data/gs_pca.rda
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/img/loading.gif
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/strapdown.js
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/countDFeByg.xls
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL/mceval.R
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/bowtieSE.param
Added  /trunk/madman/Rpacks/rain/R/rain-package.R
Added  /trunk/madman/Rpacks/TSCAN/man/lpsdata.Rd
Added  /trunk/madman/Rpacks/systemPipeR/man/GOHyperGAll.Rd
Added  /trunk/madman/Rpacks/GOsummaries/R/GOsummaries-package.R
Added  /trunk/madman/Rpacks/geecc/data/marioni.rda
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/sort_asc.png
Added  /trunk/madman/Rpacks/GOsummaries/inst/CITATION
Added  /trunk/madman/Rpacks/systemPipeR
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/jquery.tocify.min.js
Added  /trunk/madman/Rpacks/GOsummaries/R/GOsummaries.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/css/style.css
Added  /trunk/madman/Rpacks/geecc/vignettes/geecc.Rnw
Added  /trunk/madman/Rpacks/GOsummaries/src/Makevars
Added  /trunk/madman/Rpacks/seqplots/R/int_getSF.R
Added  /trunk/madman/Rpacks/seqplots/man/run.Rd
Added  /trunk/madman/Rpacks/TSCAN/man/orderscore.Rd
Added  /trunk/madman/Rpacks/rain/vignettes/rain.Rnw
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_03.png
Added  /trunk/madman/Rpacks/seqplots/tests/testthat/testGUI.R
Added  /trunk/madman/Rpacks/seqplots/R/int_heatmapPlotWrapper.R
Added  /trunk/madman/Rpacks/seqplots/R/PlotSetList-class.R
Added  /trunk/madman/Rpacks/GOsummaries/man/gosummaries.prcomp.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_04.png
Added  /trunk/madman/Rpacks/TSCAN/man/singlegeneplot.Rd
Added  /trunk/madman/Rpacks/GOsummaries/man
Added  /trunk/madman/Rpacks/GOsummaries/inst
Added  /trunk/madman/Rpacks/systemPipeR/man/catmap.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/vendor/jquery.ui.widget.js
Added  /trunk/madman/Rpacks/systemPipeR/R/AllClasses.R
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeRNAseq.Rnw
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help
Added  /trunk/madman/Rpacks/seqplots/man/imPlot2.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/img/progressbar.gif
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart
Added  /trunk/madman/Rpacks/systemPipeR/R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/strapdown.css
Added  /trunk/madman/Rpacks/GOsummaries/data/tissue_example.RData
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/ico.png
Added  /trunk/madman/Rpacks/systemPipeR/tests
Added  /trunk/madman/Rpacks/seqplots/NEWS
Added  /trunk/madman/Rpacks/geecc/R/concubfilter-class.R
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/targets.txt
Added  /trunk/madman/Rpacks/systemPipeR/man/symLink2bam.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/font
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/www/busy.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/color/hs.png
Added  /trunk/madman/Rpacks/rain/man/rain.Rd
Modified  /trunk/madman/Rpacks/bioc_3.0.manifest
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_02.png
Added  /trunk/madman/Rpacks/systemPipeR/man/qsubRun.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL
Added  /trunk/madman/Rpacks/geecc/man/filterConCub.Rd
Added  /trunk/madman/Rpacks/GOsummaries/data/metabolomic_example.RData
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_06.png
Added  /trunk/madman/Rpacks/GOsummaries/man/gosummaries.Rd
Added  /trunk/madman/Rpacks/systemPipeR/R/fastqQuality.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/DataTables/dataTables.tableTools.min.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css
Added  /trunk/madman/Rpacks/TSCAN/data/lpsdata.rda
Added  /trunk/madman/Rpacks/TSCAN/R/TSPpseudotime.R
Added  /trunk/madman/Rpacks/GOsummaries/src/findCoordinates.cpp
Added  /trunk/madman/Rpacks/rain/R/mouseLiverData.R
Added  /trunk/madman/Rpacks/systemPipeR/man/seeFastq.Rd
Added  /trunk/madman/Rpacks/systemPipeR/NAMESPACE
Added  /trunk/madman/Rpacks/seqplots/R/PlotSetPair-class.R
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/server.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/journal.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/md5.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/forward_enabled_hover.png
Added  /trunk/madman/Rpacks/systemPipeR/man/moduleload.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_04.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/color.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/sort_desc.png
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata
Added  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Added  /trunk/madman/Rpacks/systemPipeR/man/readComp.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_11.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes
Added  /trunk/madman/Rpacks/rain/data
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_04.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_01.png
Added  /trunk/madman/Rpacks/rain/data/menetRNASeqMouseLiver.rda
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui/FileManagementModal.R
Added  /trunk/madman/Rpacks/seqplots/man/heatmapPlotWrapper.Rd
Added  /trunk/madman/Rpacks/seqplots/R/zzz.R
Added  /trunk/madman/Rpacks/TSCAN/R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/mcCalcStart_calculations.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/cors/jquery.xdr-transport.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/jquery.iframe-transport.js
Added  /trunk/madman/Rpacks/seqplots/tests
Added  /trunk/madman/Rpacks/rain/DESCRIPTION
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/fastqReport.pdf
Added  /trunk/madman/Rpacks/systemPipeR/man/runCommandline.Rd
Added  /trunk/madman/Rpacks/geecc/vignettes
Added  /trunk/madman/Rpacks/seqplots/vignettes
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/vendor
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/actionbutton.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/superhero.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/mcDoParallel_plotting.R
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/tophat.param
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/modal_events.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/back_disabled.png
Added  /trunk/madman/Rpacks/TSCAN/R/preprocess.R
Added  /trunk/madman/Rpacks/TSCAN/man/difftest.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/forward_disabled.png
Added  /trunk/madman/Rpacks/geecc/man/concub-class.Rd
Added  /trunk/madman/Rpacks/GOsummaries/data/gs_limma.rda
Added  /trunk/madman/Rpacks/systemPipeR/man/SYSargs-class.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/css/jquery.fileupload-ui-noscript.css
Added  /trunk/madman/Rpacks/TSCAN/NAMESPACE
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_03.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/DataTables
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload
Added  /trunk/madman/Rpacks/seqplots/R/generic_methods.R
Added  /trunk/madman/Rpacks/GOsummaries/man/plotWordcloud.Rd
Added  /trunk/madman/Rpacks/seqplots/tests/testthat/test1.R
Added  /trunk/madman/Rpacks/seqplots/man/seqplots-generic.Rd
Added  /trunk/madman/Rpacks/systemPipeR/tests/runTests.R
Added  /trunk/madman/Rpacks/rain/R/p.est.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/LICENSE
Added  /trunk/madman/Rpacks/seqplots/R/plotAverage.R
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeVARseq.Rnw
Added  /trunk/madman/Rpacks/seqplots/inst
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/bootstrap.min.js
Added  /trunk/madman/Rpacks/geecc/R/littlehelpers.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/cors
Added  /trunk/madman/Rpacks/GOsummaries/R
Added  /trunk/madman/Rpacks/TSCAN/man/TSCAN.Rd
Added  /trunk/madman/Rpacks/seqplots/tests/test-all.R
Added  /trunk/madman/Rpacks/TSCAN/R/lpsdata.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_04.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_01.png
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/www/ajaxloaderq.gif
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/amelia.min.css
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests
Added  /trunk/madman/Rpacks/GOsummaries/vignettes
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/load_finished.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/style.css
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/bibtex.bib
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/GOslimbarplotMF.pdf
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/jquery.fileupload-fp.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_05.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/procQuick.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/font/fontawesome-webfont.eot
Added  /trunk/madman/Rpacks/seqplots/tests/testthat
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/doFileOperations.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/css/images/sort_desc_disabled.png
Added  /trunk/madman/Rpacks/GOsummaries/man/plot.gosummaries.Rd
Added  /trunk/madman/Rpacks/geecc/man/geecc-package.Rd
Added  /trunk/madman/Rpacks/seqplots/man
Added  /trunk/madman/Rpacks/GOsummaries/src/Makevars.win
Added  /trunk/madman/Rpacks/rain/R
Added  /trunk/madman/Rpacks/GOsummaries
Added  /trunk/madman/Rpacks/systemPipeR/inst/unitTests/SRR446028_1.fastq
Added  /trunk/madman/Rpacks/GOsummaries/man/add_to_slot.gosummaries.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/css
Added  /trunk/madman/Rpacks/rain/vignettes
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/jquery.fileupload.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_03.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/united.min.css
Added  /trunk/madman/Rpacks/TSCAN/man/plotpseudotime.Rd
Added  /trunk/madman/Rpacks/seqplots/R/getPlotSetArray.R
Added  /trunk/madman/Rpacks/rain/man/menetRNASeqMouseLiver.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_07.png
Added  /trunk/madman/Rpacks/geecc
Added  /trunk/madman/Rpacks/systemPipeR/inst/extdata/targetsPE.txt
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/help.html
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/readable.min.css
Added  /trunk/madman/Rpacks/GOsummaries/DESCRIPTION
Added  /trunk/madman/Rpacks/rain/R/umbCirc.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/prettify.min.js
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/renderHTMLgrid.R
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/bootstrap-responsive.min.css
Added  /trunk/madman/Rpacks/TSCAN/inst
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_01.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/jquery.lettering.js
Added  /trunk/madman/Rpacks/TSCAN/DESCRIPTION
Added  /trunk/madman/Rpacks/systemPipeR/man/filterDEGs.Rd
Added  /trunk/madman/Rpacks/TSCAN/man/TSPpseudotime.Rd
Added  /trunk/madman/Rpacks/TSCAN/man/TSCANui.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_01.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_12.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_02.png
Added  /trunk/madman/Rpacks/seqplots/README.md
Added  /trunk/madman/Rpacks/seqplots/man/plot.Rd
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/icos.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/spruce.min.css
Adds rain/ TSCAN/ GOsummaries/ geecc/ seqplots/ systemPipeR/ to the repos.
Revision: 94313
Author: m.carlson
Date: 2014-09-19T22:46:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/AnnDbObj-lowAPI.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/AnnDbPkg-checker.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/AnnDbPkg-templates-common.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
More changes to allow for graceful deprecation and defuncting of bimaps
Revision: 94312
Author: j.gadin
Date: 2014-09-19T22:05:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/detect-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: cf553ebfb7a8e16b5359bb7671426ba65f5ec573

    switched ref alt in detectAI

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-20 00:01:17 +0200
Author date: 2014-09-20 00:01:17 +0200
Revision: 94311
Author: p.kimes
Date: 2014-09-19T22:01:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/SigFuge/vignettes/SigFuge.Rnw
Modified  /trunk/madman/Rpacks/SigFuge/R/SFnormalize.R
Modified  /trunk/madman/Rpacks/SigFuge/R/SFfigure.R
Modified  /trunk/madman/Rpacks/SigFuge/R/SFlabels.R
Modified  /trunk/madman/Rpacks/SigFuge/R/SFpval.R
Modified  /trunk/madman/Rpacks/SigFuge/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ea9aa30f9f7593046372f56430bf9ed207d9c12f

    update reference

Committed by: Patrick Kimes
Author Name: Patrick Kimes
Commit date: 2014-09-19 15:00:50 -0700
Author date: 2014-09-19 15:00:50 -0700
Revision: 94310
Author: j.gadin
Date: 2014-09-19T21:58:58+00:00
Paths:
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/test_filter_heterozygots.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/mapbias-methods.R
Added  /trunk/madman/Rpacks/AllelicImbalance/data/ASEset.sim.rdata
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ReferenceBias-class.Rd
Deleted  /trunk/madman/Rpacks/AllelicImbalance/inst/extdata/hg19.chr17.fa.fai
Added  /trunk/madman/Rpacks/AllelicImbalance/man/histplot.Rd
Deleted  /trunk/madman/Rpacks/AllelicImbalance/inst/extdata/hg19.chr17.fa
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/filter-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-class.R
Added  /trunk/madman/Rpacks/AllelicImbalance/inst/extdata/hg19.chr17.subset.fa.fai
Added  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset.sim.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/inst/extdata/hg19.chr17.subset.fa
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Added  /trunk/madman/Rpacks/AllelicImbalance/data/ReferenceBias.rdata
Added  /trunk/madman/Rpacks/AllelicImbalance/man/detectAI.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/R/histplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/initialize-ReferenceBias.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/test_calc_arank.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/inferGenotypes.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/refFraction.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/data/ASEset.rdata
Added  /trunk/madman/Rpacks/AllelicImbalance/R/boxplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllelicImbalance-package.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/inference-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ReferenceBias-class.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/test_infer_genotypes.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/initialize-methods.R
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/test_refFraction.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-class.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/boxplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/refAllele.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/R/detect-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commits.

Commit information:

Commit id: d86cb2b1fe029500eeb4802165421087c602cb95

    changed fasta example data, some general doc update

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-19 23:54:32 +0200
Author date: 2014-09-19 23:54:32 +0200

Commit id: 0be964719fd44c512895a62a5eef8f40b343d634

    finished new method detectAI

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-19 15:16:45 +0200
Author date: 2014-09-19 15:16:45 +0200

Commit id: 91629d656eae87e2190791676d33c8ca9a11d681

    bugfix for refFraction and closer to finish the detectAI function

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-19 12:55:13 +0200
Author date: 2014-09-19 12:55:13 +0200

Commit id: 507971a4b22d35fceabff41e632e317f99c3ced4

    some plots and a detection method, but discovered also a bug..

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-18 23:44:10 +0200
Author date: 2014-09-18 23:44:10 +0200

Commit id: d2b80fc4ee191c2fa8b506466d6ebfff53f18297

    made ReferenceBias-class inherit SummarizedExperiments

Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-17 14:58:33 +0200
Author date: 2014-09-17 14:58:33 +0200
Revision: 94309
Author: x.zhao
Date: 2014-09-19T21:53:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/NGScopy/vignettes/NGScopy-vignette.Rnw
Modified  /trunk/madman/Rpacks/NGScopy/vignettes/Xvignette.sty
Deleted  /trunk/madman/Rpacks/NGScopy/vignettes/mdframed.sty
Updated vignette style for Ubuntu capacity.
Revision: 94307
Author: l.zhu
Date: 2014-09-19T20:53:16+00:00
Paths:
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/OfftargetAnalysis.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/OfftargetAnalysis.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/REcutDetails.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/OfftargetAnalysis.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/REcutDetails.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/REcutDetails.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/Summary.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/pairedgRNAs.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/RIPK1stopallgRNAs.fa
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/pairedgRNAs.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/RIPK1stopallgRNAs.fa
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/Summary.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/pairedgRNAs.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/RIPK1stopallgRNAs.fa
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn/mRIPK1stop.gbk
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn/mRIPK1stop.gbk
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon/mRIPK1stop.gbk
added more test cases and test files
Revision: 94306
Author: l.zhu
Date: 2014-09-19T20:50:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withRE/pairedgRNAs.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/gRNAProvidedSearchNOoffTarget/OfftargetAnalysis.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withRE/pairedgRNAs.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/WithorgAnn
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOorgAnn
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/gRNAProvidedSearchNOoffTarget/Summary.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse/NOTannotateExon
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysis.R
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withoutRE/REcutDetails.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/RIPK1stop.fa
Modified  /trunk/madman/Rpacks/CRISPRseek/R/filterOffTarget.R
Added  /trunk/madman/Rpacks/CRISPRseek/inst/NEWS
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/REcutDetails.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/unitTests/test_mouse_orgAnn_annotateExon.R
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withoutRE/pairedgRNAs.xls
Added  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/testMouse
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/pairedSearch/withRE/REcutDetails.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/Summary.xls
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/extdata/unPairedSearch/withoutRE/pairedgRNAs.xls
fixed bug for number of Ts in the last 4 positon of gRNA and order of xMMdistance2PAM columns in summary file, and also made orgAnn optional
Revision: 94305
Author: r.castelo
Date: 2014-09-19T19:48:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/NAMESPACE
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetwork-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/qpgraph/R/AllGeneric.R
Added graph() method for eQTLnetwork objects.
Revision: 94304
Author: r.castelo
Date: 2014-09-19T19:10:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Increase version to 1.99.0 to bump to 2.0 in the next release.
Revision: 94302
Author: p.shannon
Date: 2014-09-19T18:14:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/ui.R
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/server.R
added printf definition to both files, removed commented out HTML command
Revision: 94301
Author: p.shannon
Date: 2014-09-19T18:12:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
unsuccessful attempt to get background color of selected rows to color properly
Revision: 94300
Author: p.shannon
Date: 2014-09-19T18:11:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/ui.R
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/server.R
versions used in first public installation, on bell
Revision: 94299
Author: m.love
Date: 2014-09-19T17:53:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/R/plots.R
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/beginner.Rnw
plotPCA should give the percent var as attr
Revision: 94298
Author: m.jiang
Date: 2014-09-19T17:15:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/DESCRIPTION
Added  /trunk/madman/Rpacks/openCyto/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: a00cec4428958167ded02484056965bee6a38eb6

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-19 10:14:49 -0700
Author date: 2014-09-19 10:14:49 -0700

Commit id: 400d09214165930ca4566d25e92e21cbdea024c2

    bump version

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-19 10:14:40 -0700
Author date: 2014-09-19 10:14:40 -0700

Commit id: 5b91b561fefdebf95eb95b24ef32e2622ed2b935

    Create CITATION

    Add relevant citation to package.

Committed by: mikejiang
Author Name: Greg Finak
Commit date: 2014-09-19 10:14:17 -0700
Author date: 2014-09-19 09:49:22 -0700
Revision: 94297
Author: r.castelo
Date: 2014-09-19T17:05:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetwork-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Added option gene.loc to alleQTL().
Revision: 94295
Author: n.hayden
Date: 2014-09-19T16:31:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGseq/DESCRIPTION
update Likun's email address
Revision: 94294
Author: n.hayden
Date: 2014-09-19T16:29:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/ASEB/DESCRIPTION
update Likun's email address
Revision: 94293
Author: c.beauparlant
Date: 2014-09-19T15:28:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagene/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c4ed89cde8ddccfcc858b631daa94e9b6314adf6

    DESCRIPTION: version bump

    Signed-off-by: Charles Joly Beauparlant 

Committed by: Charles Joly Beauparlant
Author Name: Charles Joly Beauparlant
Commit date: 2014-09-19 11:28:50 -0400
Author date: 2014-09-19 11:28:50 -0400
Revision: 94292
Author: c.beauparlant
Date: 2014-09-19T15:07:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagene/R/parseHelpers.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f1f503f710cc4a1a8d29e992e9f643d1fffb50e3

    R/parseHelpers.R: corrected a bug that caused scaling to skip a position with specific domain values/domain combinations

    Signed-off-by: Charles Joly Beauparlant 

Committed by: Charles Joly Beauparlant
Author Name: Charles Joly Beauparlant
Commit date: 2014-09-19 11:07:33 -0400
Author date: 2014-09-19 11:07:33 -0400
Revision: 94290
Author: rscharpf
Date: 2014-09-19T14:42:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-TrioSetList.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinDistExperiment-class.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/acf2.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/Makefile
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/concordance.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/zzz.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/PennParam.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_calculateMindist.R
Added  /trunk/madman/Rpacks/MinimumDistance/inst/extdata/md_granges.rds
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinimumDistance.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/isDenovo.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-matrix.R
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_callDenovoSegments.R
Modified  /trunk/madman/Rpacks/MinimumDistance/man/TrioSet-class.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/xyplotTrio.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/computeBayesFactor.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_PedigreeViews.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/exampleTrioSetList.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/coercion-methods.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-ShallowSimpleList.R
Modified  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_posteriorCalls.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-SummarizedExperiment.R
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/.gitignore
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_MinDistExperiment.R
Modified  /trunk/madman/Rpacks/MinimumDistance/R/AllGenerics.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-ILimit.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/help.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-FilterParamMD.R
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/stackRangedDataList.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/data/map.segs.rda
Deleted  /trunk/madman/Rpacks/MinimumDistance/R/methods-RangedData.R
Modified  /trunk/madman/Rpacks/MinimumDistance/NAMESPACE
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinDistGRanges.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/nMAD.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_Pedigree-class.R
Added  /trunk/madman/Rpacks/MinimumDistance/.gitignore
Added  /trunk/madman/Rpacks/MinimumDistance/man/md_gr.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/man/TrioSet.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/R/datasets.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-ParentOffspring.R
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-AssayData.R
Deleted  /trunk/madman/Rpacks/MinimumDistance/data/md.segs.rda
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/gcSubtract.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-MinDistGRanges.R
Modified  /trunk/madman/Rpacks/MinimumDistance/man/TrioSetListLD.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_FilterParam.R
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-AnnotatedDataFrame.R
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/correspondingCall.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/AllClasses.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/ParentOffspring-class.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-ff_array.R
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-TrioSet.R
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_quads.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-FileViews.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinDistGRanges-class.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/generator-funs.R
Modified  /trunk/madman/Rpacks/MinimumDistance/man/mad2.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/man/Pedigree.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/mad-methods.R
Modified  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_TrioSetList.R
Modified  /trunk/madman/Rpacks/MinimumDistance/vignettes/MinimumDistance.Rnw
Modified  /trunk/madman/Rpacks/MinimumDistance/man/calculateMindist.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/man/TrioSetList-class.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinDistParam.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/functions.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-MinDistExperiment.R
Added  /trunk/madman/Rpacks/MinimumDistance/NEWS
Deleted  /trunk/madman/Rpacks/MinimumDistance/data/lrr.segs.rda
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-list.R
Added  /trunk/madman/Rpacks/MinimumDistance/vignettes/.gitignore
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_SnpArrayExperiment.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/range-ILimit-method.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/trioSetListExample.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-PennParam.R
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_few_markers.R
Modified  /trunk/madman/Rpacks/MinimumDistance/R/segment2-methods.R
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-Pedigree.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/mindist.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/narrow.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinDistExperiment.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/R/lattice-methods.R
Added  /trunk/madman/Rpacks/MinimumDistance/.gigignore
Added  /trunk/madman/Rpacks/MinimumDistance/R/defunct.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-MinDistParam.R
Added  /trunk/madman/Rpacks/MinimumDistance/data/md_exp.rda
Added  /trunk/madman/Rpacks/MinimumDistance/man/md_exp.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/MAP.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/xypanelTrio.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-MDRanges.R
Added  /trunk/madman/Rpacks/MinimumDistance/R/coercion-methods.R
Modified  /trunk/madman/Rpacks/MinimumDistance/man/segment2.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/TrioSetList.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/pedigreeName.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/filterExperiment.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/man/Pedigree-class.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/data/md_gr.rda
Added  /trunk/madman/Rpacks/MinimumDistance/man/Defunct.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/denovo.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/FilterParamMD-class.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/MinDistParam-class.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/callDenovoSegments.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/lrr.segs.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/MAP2.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/Deprecated.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/R/methods-MinDistPosterior.R
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/coerce-methods.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/phenoData.Rd
Added  /trunk/madman/Rpacks/MinimumDistance/man/MDRanges-class.Rd
Modified  /trunk/madman/Rpacks/MinimumDistance/DESCRIPTION
Added  /trunk/madman/Rpacks/MinimumDistance/inst/unitTests/test_rdsViews.R
Added  /trunk/madman/Rpacks/MinimumDistance/man/ParentOffspringList-class.Rd
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/annotatedDataFrameFrom-methods.Rd
setting up git-svn bridge
Revision: 94289
Author: rscharpf
Date: 2014-09-19T14:41:20+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/defunct.Rd
remove defunct.Rd
Revision: 94288
Author: rscharpf
Date: 2014-09-19T14:39:55+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MinimumDistance/man/trioSetList.Rd
removed trioSetList.Rd
Revision: 94287
Author: t.hardcastle
Date: 2014-09-19T14:38:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/riboSeqR/vignettes/riboSeq.Rnw
Modified  /trunk/madman/Rpacks/riboSeqR/DESCRIPTION
v 0.99.17 updated name in vignette.
Revision: 94286
Author: rscharpf
Date: 2014-09-19T14:23:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/man/viterbi2Wrapper.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/numberFeatures.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_HmmGRanges.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-SnpDataFrame.R
Added  /trunk/madman/Rpacks/VanillaICE/man/sweepMode.Rd
Added  /trunk/madman/Rpacks/VanillaICE/R/methods-FilterParam.R
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/FinalReport6841.csv
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/FinalReport1675.csv
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/snp_exp.rds
Added  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_ArrayViews.R
Added  /trunk/madman/Rpacks/VanillaICE/man/parseSourceFile.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/cnvFilter.Rd
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/SNP_info.csv
Added  /trunk/madman/Rpacks/VanillaICE/man/plotting.Rd
Added  /trunk/madman/Rpacks/VanillaICE/R/methods-HMMList.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/read.bsfiles.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/segs.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/data/hmmResults.rda
Added  /trunk/madman/Rpacks/VanillaICE/man/viewports.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/matrixOrNULL-class.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Added  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_FilterParam.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/robust-statistics.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/IO.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/emissionParam.Rd
Added  /trunk/madman/Rpacks/VanillaICE/data/snp_exp.rda
Modified  /trunk/madman/Rpacks/VanillaICE/vignettes/crlmmDownstream.Rnw
Added  /trunk/madman/Rpacks/VanillaICE/man/snp_exp.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/dropSexChrom.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/man/start-oligoSnpSet-method.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/probability.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/state-methods.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/HMM.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/LogLik.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/dropDuplicatedMapLocs.Rd
Added  /trunk/madman/Rpacks/VanillaICE/R/methods-HmmTrellisParam.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-Viterbi.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/updates.R
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/crlmmResults.rda
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-EmissionParam.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/functions.R
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/FinalReport1686.csv
Modified  /trunk/madman/Rpacks/VanillaICE/src/viterbi.c
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-TransitionParam.R
Added  /trunk/madman/Rpacks/VanillaICE/man/SnpExperiment.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/LRRandBAF.txt
Added  /trunk/madman/Rpacks/VanillaICE/man/hmm2.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/calculateEmission.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/R/hmm-methods.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/VanillaICE.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/SnpGRanges.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/R/AllClasses.R
Added  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/TestData.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/AllGenerics.R
Added  /trunk/madman/Rpacks/VanillaICE/man/TransitionParam.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_hmm.R
Added  /trunk/madman/Rpacks/VanillaICE/man/snpArrayAssays.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/vignettes/ice.bib
Added  /trunk/madman/Rpacks/VanillaICE/man/LogLik-class.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/updateHmmParams.Rd
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/FinalReport6903.csv
Added  /trunk/madman/Rpacks/VanillaICE/man/parsedPath.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/man/BeadStudioSet.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/Deprecated.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/NA_filter.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/CopyNumScanParams.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_viterbi.R
Added  /trunk/madman/Rpacks/VanillaICE/R/methods-HMM.R
Modified  /trunk/madman/Rpacks/VanillaICE/vignettes/VanillaICE.Rnw
Added  /trunk/madman/Rpacks/VanillaICE/man/Viterbi-methods.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/xygrid.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/filters.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/FilterParam-class.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/R/help.R
Added  /trunk/madman/Rpacks/VanillaICE/man/baumWelchUpdate.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/HMMList.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/man/rescale.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/pd.mapping250k.styConf.rda
Added  /trunk/madman/Rpacks/VanillaICE/man/oligoSetList.Rd
Added  /trunk/madman/Rpacks/VanillaICE/R/methods-IdiogramParams.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-HmmParam.R
Added  /trunk/madman/Rpacks/VanillaICE/man/emission.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/man/icePlatforms.Rd
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/FinalReport1664.csv
Added  /trunk/madman/Rpacks/VanillaICE/man/Defunct.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/oligosetForUnitTest.rda
Modified  /trunk/madman/Rpacks/VanillaICE/R/datasets.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/HmmGRanges-class.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/threshold.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/genomewidesnp6Conf.rda
Added  /trunk/madman/Rpacks/VanillaICE/inst/extdata/FinalReport6872.csv
Added  /trunk/madman/Rpacks/VanillaICE/man/ArrayViews-class.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/sourcePaths.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/pd.mapping250k.nspConf.rda
Added  /trunk/madman/Rpacks/VanillaICE/man/HmmTrellisParam.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_HmmParam.R
Added  /trunk/madman/Rpacks/VanillaICE/man/IdiogramParams-class.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/HmmParam.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/man/hmmResults.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/man/SnpArrayExperiment-class.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-LogLik.R
Added  /trunk/madman/Rpacks/VanillaICE/man/doUpdate.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_constraints.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/constraints.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/scripts/crlmmDownstream.Rnw
Added  /trunk/madman/Rpacks/VanillaICE/man/EmissionParam-methods.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/R/methods-GStudioScanParams.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/defunct.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-HmmGRanges.R
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/bset.rds
Modified  /trunk/madman/Rpacks/VanillaICE/NAMESPACE
Added  /trunk/madman/Rpacks/VanillaICE/man/LowLevelSummaries.Rd
Added  /trunk/madman/Rpacks/VanillaICE/man/IdiogramParam-class.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-ArrayViews.R
Added  /trunk/madman/Rpacks/VanillaICE/man/HMMList-class.Rd
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_oligoSetList.R
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_read_bsfiles.R
Deleted  /trunk/madman/Rpacks/VanillaICE/man/calculateViterbi.Rd
Deleted  /trunk/madman/Rpacks/VanillaICE/inst/extdata/genome_studio.csv
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-SnpArrayExperiment.R
Added  /trunk/madman/Rpacks/VanillaICE/man/getHmmParams.Rd
Added  /trunk/madman/Rpacks/VanillaICE/R/methods-CopyNumScanParams.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 18 commits.

Commit information:

Commit id: 1aa2cb5e2d9514013f970eaf8705290a27189a1b

    Update documentation.  Parameter class for plotting trellis.  Methods for plotting idiograms.

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-19 10:16:15 -0400
Author date: 2014-09-19 10:16:15 -0400

Commit id: 945c9a765a1936b6a43286fc4b0f563f9f8b994d

    Updates to documentation, ArrayViews methods, and vignette.

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-15 09:20:06 -0400
Author date: 2014-09-15 09:20:06 -0400

Commit id: f3088ed9b795d27078e5997751dccaf44aef11a7

    Update grangesData to subset SummarizedExperiment columns according to the id labels in the granges object

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-08 20:40:08 -0400
Author date: 2014-09-08 20:40:08 -0400

Commit id: bb7fcf08b54839fd3286b74e0664354040cdf33e

    Add HMMList class. hmm2 does not store the emission matrix when processing multiple samples

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-05 20:51:18 -0400
Author date: 2014-09-05 20:51:18 -0400

Commit id: 7b49dad964af7c320937cc8c7b5b5c0cd7201697

    Updates to documentation / man pages

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-08-30 08:21:31 -0400
Author date: 2014-08-30 08:21:31 -0400

Commit id: 68b46d76ee1cb02c6d5ce6661aa2aaa72be5a4a3

    commit all man files.  Add cnvFilter family of methods

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-08-01 08:03:39 -0400
Author date: 2014-08-01 08:03:39 -0400

Commit id: 34c07a27aa3792ba1738bda31696a795f0f58fe9

    Add methods for FilterParam class

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-30 21:12:58 -0400
Author date: 2014-07-30 21:12:58 -0400

Commit id: b97b1ff5a671be6419ac072bfab5884dc1b2e8d0

    Defined HMM class and several accessors. This class contains the GRanges object, as well as the emission probabilities.

    Will need something more efficient when looping over samples...

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-30 21:12:25 -0400
Author date: 2014-07-30 21:12:25 -0400

Commit id: f7d1fa2c086c30b339ac21595a681d4f9a59a535

    update document of methods and functions

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-26 12:46:44 -0400
Author date: 2014-07-26 12:46:44 -0400

Commit id: 833977f054a8f9d24b6ca24ffd0f5f3748003946

    Added documentation.  Remove unnecessary exports

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-25 14:36:05 -0400
Author date: 2014-07-25 14:36:05 -0400

Commit id: 9f5e28cb85297826323cb8888868989be96f6a08

    emission probabilities for BAFs are weighted by Pr(HOM)*unif + Pr(Het)*emission

    Simplified transition probability matrix in viterbi2

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-24 11:39:32 -0400
Author date: 2014-07-24 11:39:32 -0400

Commit id: 934e5925c931312fe96e3d025671095211c6f9e3

    Add code for computing a posterior probability for a given segment

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-23 11:43:03 -0400
Author date: 2014-07-23 11:43:03 -0400

Commit id: 5d8f38519351ab5c43e3c7634442eaaf7cac6841

    passes unit tests

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-19 10:02:46 -0400
Author date: 2014-07-19 10:02:46 -0400

Commit id: 7a67ea9359f03ddeb5306bc0609f7979286505e6

    Bug fix for tempering variable.  Had 1/temper * dnorm + (1-1/temper) * dunif

    Should have been (1-1/tmper) * dnorm + 1/temper*dunif

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-18 12:52:34 -0400
Author date: 2014-07-18 12:52:34 -0400

Commit id: 1e6d779383055c58e4062f904a6cc95a3b56a692

    Move NA_filter() inside .hmm function

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-16 09:50:04 -0400
Author date: 2014-07-16 09:50:04 -0400

Commit id: 9994b75f9d0c6ae4b8312bd62faa0336757f3574

    Fix bug in emission updates (remove d/d+dens_unif)

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-16 06:03:49 -0400
Author date: 2014-07-16 06:03:49 -0400

Commit id: 8ecb35ae0270017b412329481f4b8e2e7263fe76

    Set default of temper variable in EmissionParam to 100

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-16 05:45:29 -0400
Author date: 2014-07-16 05:45:29 -0400

Commit id: 617124f4752e1a6fce217ffbdd0e7fc00a914618

    Removed proportionOutlier. The 'temper' parameter has the same purpose.

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-07-15 21:06:32 -0400
Author date: 2014-07-15 21:06:32 -0400
Revision: 94285
Author: rscharpf
Date: 2014-09-19T14:22:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/crlmm/DESCRIPTION
Modified  /trunk/madman/Rpacks/crlmm/inst/scripts/AffyGW.Rnw
Modified  /trunk/madman/Rpacks/crlmm/inst/scripts/copynumber.Rnw
Modified  /trunk/madman/Rpacks/crlmm/R/methods-CNSet.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 736588e3d47fd58358f61ce2241bb2c85b4d9a0c

     update to vignette to process previously unevaluated codechunks

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-19 10:14:04 -0400
Author date: 2014-09-19 10:14:04 -0400
Revision: 94284
Author: m.iterson
Date: 2014-09-19T14:07:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/MethylAid/R/ui.R
Modified  /trunk/madman/Rpacks/MethylAid/DESCRIPTION
Modified  /trunk/madman/Rpacks/MethylAid/inst/MethylAid/server.R
Modified  /trunk/madman/Rpacks/MethylAid/inst/MethylAid/ui.R
added package version to app header
Revision: 94283
Author: p.moulos
Date: 2014-09-19T13:41:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/metaseqR/NAMESPACE
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.stat.R
Modified  /trunk/madman/Rpacks/metaseqR/inst/metaseqr_report.html
Added  /trunk/madman/Rpacks/metaseqR/man/get.ucsc.query.Rd
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.util.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.plot.R
Added  /trunk/madman/Rpacks/metaseqR/man/get.gc.content.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/metaseqr.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/get.gene.attributes.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/get.ucsc.annotation.Rd
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.main.R
Modified  /trunk/madman/Rpacks/metaseqR/vignettes/metaseqr-pdf.Rnw
Modified  /trunk/madman/Rpacks/metaseqR/man/get.annotation.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/get.ucsc.organism.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/load.bs.genome.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/reduce.gene.data.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/construct.gene.model.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/get.bs.organism.Rd
Modified  /trunk/madman/Rpacks/metaseqR/DESCRIPTION
Added  /trunk/madman/Rpacks/metaseqR/man/get.ucsc.credentials.Rd
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.argcheck.R
Modified  /trunk/madman/Rpacks/metaseqR/inst/NEWS
Added  /trunk/madman/Rpacks/metaseqR/man/get.ensembl.annotation.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/get.exon.attributes.Rd
Fixed bugs with UCSC annotation retrieval. Added details regarding the number of genes returned by each algorithm when conducting combined analysis. Fixed minor bug with warning level logging. Added partial support for new hg38 human genome version and fixed broken Ensembl annotation fetches because of this new version. Fixed a small bug that caused incomplete sets of mean-difference and mean-variance plots.
Revision: 94282
Author: r.castelo
Date: 2014-09-19T12:40:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetwork-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Added geneNames() and markerNames() methods for eQTLnetwork objects.
Revision: 94279
Author: r.castelo
Date: 2014-09-19T08:58:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetwork-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Added cieQTL() method for eQTLnetwork objects.
Revision: 94278
Author: x.zheng
Date: 2014-09-19T08:49:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/NEWS
Modified  /trunk/madman/Rpacks/SeqArray/R/AllUtilities.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 8614095de31c2d4e4496fa69c3773c91c0bd47ea

    SeqArray_1.5.1_Update

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-09-19 01:49:11 -0700
Author date: 2014-09-19 01:49:11 -0700
Revision: 94277
Author: j.waage
Date: 2014-09-19T08:43:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/spliceR/DESCRIPTION
Version updated in DESCRIPTION
Revision: 94275
Author: j.waage
Date: 2014-09-19T08:35:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/spliceR/R/annotatePTC.R
Modified  /trunk/madman/Rpacks/spliceR/man/prepareCuff.Rd
Fixed minor position bugs in annotatePTC()
Revision: 94273
Author: x.zheng
Date: 2014-09-19T08:18:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/man/seqVCF2GDS.Rd
Deleted  /trunk/madman/Rpacks/SeqArray/src/dString.h
Deleted  /trunk/madman/Rpacks/SeqArray/src/Makevars.win
Modified  /trunk/madman/Rpacks/SeqArray/NAMESPACE
Modified  /trunk/madman/Rpacks/SeqArray/README.md
Modified  /trunk/madman/Rpacks/SeqArray/src/ConvGDS2VCF.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/ConvVCF2GDS.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/SeqArray.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/Makevars
Deleted  /trunk/madman/Rpacks/SeqArray/src/dType.h
Modified  /trunk/madman/Rpacks/SeqArray/src/ReadByVariant.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/Common.h
Modified  /trunk/madman/Rpacks/SeqArray/R/AllUtilities.R
Modified  /trunk/madman/Rpacks/SeqArray/R/SeqVarGDSClass-accessors.R
Deleted  /trunk/madman/Rpacks/SeqArray/src/CoreGDSLink.cpp
Modified  /trunk/madman/Rpacks/SeqArray/NEWS
Added  /trunk/madman/Rpacks/SeqArray/src/R_SeqArray.c
Modified  /trunk/madman/Rpacks/SeqArray/tests/test.R
Deleted  /trunk/madman/Rpacks/SeqArray/src/CoreGDSLink.h
Modified  /trunk/madman/Rpacks/SeqArray/DESCRIPTION
Deleted  /trunk/madman/Rpacks/SeqArray/src/CoreDEF.h
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: babe3d707334fff3aeb4332dc63d15f1a8762566

    SeqArray_1.5.1

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-09-19 01:18:38 -0700
Author date: 2014-09-19 01:18:38 -0700
Revision: 94272
Author: b.phipson
Date: 2014-09-19T07:00:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/DESCRIPTION
Bumped package version to 0.99.8
Revision: 94271
Author: jq.sun
Date: 2014-09-19T05:55:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/R/TCC.estimateDE.SAMseq.R
Modified  /trunk/madman/Rpacks/TCC/R/YAYOI.R
Modified  /trunk/madman/Rpacks/TCC/NEWS
Modified  /trunk/madman/Rpacks/TCC/DESCRIPTION
minor change
Revision: 94270
Author: d.henderson
Date: 2014-09-19T04:27:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/src/pedtemplate.cc
Let's try this
Revision: 94267
Author: smyth
Date: 2014-09-19T02:03:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/R/geneset-roast.R
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/diffSplice.Rd
Modified  /trunk/madman/Rpacks/limma/R/diffSplice.R
Modified  /trunk/madman/Rpacks/limma/inst/NEWS.Rd
19 Sep 2014: limma 3.21.18

- new argument 'robust' for diffSplice(), giving access to robust
  empirical Bayes variance moderation.
Revision: 94266
Author: x.zheng
Date: 2014-09-19T02:03:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPRelate/DESCRIPTION
Modified  /trunk/madman/Rpacks/SNPRelate/R/Conversion.R
Modified  /trunk/madman/Rpacks/SNPRelate/man/snpgdsBED2GDS.Rd
Modified  /trunk/madman/Rpacks/SNPRelate/NEWS
Modified  /trunk/madman/Rpacks/SNPRelate/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 705bfe8a4a26c76b908a7723199bd80c18dd2bc7

    Update snpgdsBED2GDS

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-09-18 19:03:34 -0700
Author date: 2014-09-18 19:03:34 -0700
Revision: 94265
Author: v.obenchain
Date: 2014-09-19T01:48:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/R/bplapply-methods.R
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpaggregate.Rd
Modified  /trunk/madman/Rpacks/BiocParallel/R/bpaggregate-methods.R
Modified  /trunk/madman/Rpacks/BiocParallel/man/bplapply.Rd
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
bpaggregate

- enhance man page
- modify bpaggregate,function,BiocParam-method to run in parallel
Revision: 94263
Author: smyth
Date: 2014-09-19T00:40:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/R/geneset-roast.R
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/R/lmfit.R
19 Sep 2014: limma 3.21.17

- getEAWP() will now find a weights matrix in an ExpressionSet object
  if it exists.

- The contrast argument to roast() and mroast() can now optionally be
  a character string giving a column name of the design matrix.
Revision: 94262
Author: b.phipson
Date: 2014-09-19T00:32:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/man/contrasts.varFit.Rd
Fixed example.
Revision: 94257
Author: m.carlson
Date: 2014-09-19T00:06:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/AnnDbPkg-templates-common.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Deprecates and defuncts bimaps and keytypes.
Revision: 94256
Author: mtmorgan
Date: 2014-09-18T23:45:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/man/scanTabix.Rd
Modified  /trunk/madman/Rpacks/Rsamtools/src/tabixfile.c
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
report scanTabix error code
Revision: 94255
Author: mtmorgan
Date: 2014-09-18T23:32:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/bvbiome/DESCRIPTION
package rename
Revision: 94254
Author: mtmorgan
Date: 2014-09-18T23:30:01+00:00
Paths:
Added  /trunk/madman/Rpacks/bvbiome
Deleted  /trunk/madman/Rpacks/microbiome
move 'microbiome' package to 'bvbiome'
Revision: 94253
Author: p.shannon
Date: 2014-09-18T23:01:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/server.R
before recreating standard separate ui.R and server.R, deploying to bell
Revision: 94252
Author: m.jiang
Date: 2014-09-18T22:41:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/tests/expect_result/layoutGraph_gh.rds
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingHierarchy-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/vignettes/HowToMergeGatingSet.Rmd
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: ee97938a802ca4abc9cf2b6f8af241aaa927d369

    annotate bool gate in plot method

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-18 15:40:34 -0700
Author date: 2014-09-18 15:40:34 -0700

Commit id: 56ab4956e9f4cf67d919cab045e3c12a191cfadf

    annotate bool gate in plot method

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-18 15:33:00 -0700
Author date: 2014-09-18 15:33:00 -0700

Commit id: 14256cde281459c15934f8d4d345bdd9f143a983

    add HowToMergeGatingSet.Rmd

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-17 16:03:58 -0700
Author date: 2014-09-17 15:47:47 -0700
Revision: 94251
Author: g.finak
Date: 2014-09-18T22:38:47+00:00
Paths:
Added  /trunk/madman/Rpacks/MIMOSA/man/asinh_trans.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/NAMESPACE
Modified  /trunk/madman/Rpacks/MIMOSA/R/helperMethods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 98a18426ace633069f8a367b2cb9c45a19dd3626

    added arcsinh transform for ggplot2

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-09-18 15:38:38 -0700
Author date: 2014-09-18 15:38:38 -0700
Revision: 94250
Author: g.finak
Date: 2014-09-18T22:32:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/MIMOSA/man/fdr.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/NAMESPACE
Modified  /trunk/madman/Rpacks/MIMOSA/man/MIMOSA-package.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/MDMix.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/ICS.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/MIMOSAExpressionSet.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/fitMCMC.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/countsTable.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/MIMOSA.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/R/helperMethods.R
Modified  /trunk/madman/Rpacks/MIMOSA/man/ConstructMIMOSAExpressionSet.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/MIMOSAResult-class.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/pData.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/print.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/volcanoPlot.Rd
Added  /trunk/madman/Rpacks/MIMOSA/man/combine.MIMOSA.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/DESCRIPTION
Added  /trunk/madman/Rpacks/MIMOSA/man/boxplot.MIMOSAResultList.Rd
Modified  /trunk/madman/Rpacks/MIMOSA/man/MIMOSA-accessors.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 993f891bb3d33b24a07a429505bfcad16701170c

    document boxplot

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-09-18 15:32:12 -0700
Author date: 2014-09-18 15:32:12 -0700

Commit id: 6ca62c50f7eaa2fdec347c5a7ae90fa3e65e1aca

    added documentation for combine

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-09-18 15:31:22 -0700
Author date: 2014-09-18 15:31:22 -0700

Commit id: 94ba0243b09f1d851fdf2957ff405bcad07d2f62

    added methods to make boxplots and combine results

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-09-18 15:30:57 -0700
Author date: 2014-09-18 15:30:57 -0700
Revision: 94247
Author: m.jiang
Date: 2014-09-18T21:10:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/R/gtMethod-methods.R
Modified  /trunk/madman/Rpacks/openCyto/R/pluginFramework.R
Modified  /trunk/madman/Rpacks/openCyto/R/preprocessing-method.R
Modified  /trunk/madman/Rpacks/openCyto/DESCRIPTION
Added  /trunk/madman/Rpacks/openCyto/man/filterObject-logicalFilterResult-method.Rd
Modified  /trunk/madman/Rpacks/openCyto/R/AllClasses.R
Modified  /trunk/madman/Rpacks/openCyto/R/wrapper-functions.R
Modified  /trunk/madman/Rpacks/openCyto/man/add.Rd
Modified  /trunk/madman/Rpacks/openCyto/inst/tests/test-pluginFramework.R
Modified  /trunk/madman/Rpacks/openCyto/R/add.R
Modified  /trunk/madman/Rpacks/openCyto/R/functions.R
Modified  /trunk/madman/Rpacks/openCyto/R/gating-methods.R
Modified  /trunk/madman/Rpacks/openCyto/NAMESPACE
Commit made by the Bioconductor Git-SVN bridge.
Consists of 10 commits.

Commit information:

Commit id: ab562ca2039c6913854a67d0f8ce1676e23e5a0d

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-18 10:28:35 -0700
Author date: 2014-09-18 10:28:35 -0700

Commit id: 85ab5035ed8ddd379e117dbf1c87a195a5ede0eb

    add man/filterObject-logicalFilterResult-method.Rd

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-18 10:28:23 -0700
Author date: 2014-09-18 10:28:23 -0700

Commit id: ba57a255b3e68a23b07be19475c393bd4221ee01

    parse 'subSample' argument from 'gating_args' column in csv template to allow subsampling the data prior to gating.

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-09-03 14:25:32 -0700
Author date: 2014-09-02 17:03:08 -0700

Commit id: b1c3aa554bb0689b43f2fc2d70e03da922cc4042

    fix docs

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-08-25 16:46:23 -0700
Author date: 2014-08-25 16:46:23 -0700

Commit id: cc3d8565c972eb0b5308cafb8aa219a40b83a7ec

    update according to the latest enhancement from ncdfFlow

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-08-19 14:18:30 -0700
Author date: 2014-08-19 14:18:30 -0700

Commit id: d3c08794f31193cb0e3439b44c3f57585d7da790

    merge from trunk

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-23 15:38:44 -0700
Author date: 2014-07-23 15:38:44 -0700

Commit id: 32e197f485c98ffca346c9ba4e063f28996e25d0

    1. change gating_wrapper to gating_adaptor 2. do the strict matching for refGate-like method name

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-21 16:14:10 -0700
Author date: 2014-07-21 16:14:10 -0700

Commit id: 7fd8f10c069e7fef15fd0695aaa6128b76265ba7

    add method for multipleFitlerResult. #73

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-14 16:17:56 -0700
Author date: 2014-07-14 14:25:27 -0700

Commit id: c1b59db6f3e8a58e59a36d6868654a3bb2102c1a

    fix the warning in registerPlugins

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-14 10:10:59 -0700
Author date: 2014-07-14 10:10:59 -0700

Commit id: 0c70dac7bd3a5cf9b53f6d5546de2d241a044a97

    support multi-dimensions in framework by deprecating x,y with channels. #73

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-11 16:49:26 -0700
Author date: 2014-07-11 16:49:26 -0700
Revision: 94246
Author: s.arora
Date: 2014-09-18T21:10:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
fix spelling

correct spelling of PrincipalComponent.

Source Code & Build Reports »

Source code is stored in svn (user: readonly, pass: readonly).

Software packages are built and checked nightly. Build reports:

 

Development Version»

Bioconductor packages under development:


Developer Resources:

Fred Hutchinson Cancer Research Center