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: 121617
Author: t.yuan
Date: 2016-10-01T18:12:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChAMP/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChAMP/NAMESPACE
Deleted  /trunk/madman/Rpacks/ChAMP/R/BMIQ.R
Added  /trunk/madman/Rpacks/ChAMP/R/Block.GUI.R
Added  /trunk/madman/Rpacks/ChAMP/R/CpG.GUI.R
Added  /trunk/madman/Rpacks/ChAMP/R/DMR.GUI.R
Modified  /trunk/madman/Rpacks/ChAMP/R/EstDimRMTv2.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/GenPlot.R
Added  /trunk/madman/Rpacks/ChAMP/R/MVP.GUI.R
Added  /trunk/madman/Rpacks/ChAMP/R/QC.GUI.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/aprior.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/bprior.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/build.design.R
Added  /trunk/madman/Rpacks/ChAMP/R/champ.BMIQ.R
Added  /trunk/madman/Rpacks/ChAMP/R/champ.Block.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.CNA.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.ComBat.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.DMR.R
Added  /trunk/madman/Rpacks/ChAMP/R/champ.EpiMod.R
Added  /trunk/madman/Rpacks/ChAMP/R/champ.GSEA.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.MVP.R
Added  /trunk/madman/Rpacks/ChAMP/R/champ.QC.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.SVD.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/champ.TrueMethyl.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/champ.bedfile.R
Added  /trunk/madman/Rpacks/ChAMP/R/champ.impute.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.load.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.norm.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.process.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.refbase.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.reffree.R
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.runCombat.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/design.mat.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/it.sol.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/list.batch.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/plotThreshold.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/postmean.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/postvar.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/projectWBC.R
Deleted  /trunk/madman/Rpacks/ChAMP/R/thdens.R
Added  /trunk/madman/Rpacks/ChAMP/R/zzz.R
Modified  /trunk/madman/Rpacks/ChAMP/build/vignette.rds
Modified  /trunk/madman/Rpacks/ChAMP/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/ChAMP/inst/doc/ChAMP.R
Added  /trunk/madman/Rpacks/ChAMP/inst/doc/ChAMP.Rmd
Deleted  /trunk/madman/Rpacks/ChAMP/inst/doc/ChAMP.Rnw
Added  /trunk/madman/Rpacks/ChAMP/inst/doc/ChAMP.html
Deleted  /trunk/madman/Rpacks/ChAMP/inst/doc/ChAMP.pdf
Added  /trunk/madman/Rpacks/ChAMP/man/Block.GUI.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/ChAMP-package.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/CpG.GUI.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/DMR.GUI.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/MVP.GUI.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/QC.GUI.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/champ.Block.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.CNA.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.DMR.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/champ.EpiMod.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/champ.GSEA.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.MVP.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/champ.QC.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.SVD.Rd
Deleted  /trunk/madman/Rpacks/ChAMP/man/champ.TrueMethyl.Rd
Added  /trunk/madman/Rpacks/ChAMP/man/champ.impute.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.load.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.norm.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.process.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.refbase.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.reffree.Rd
Modified  /trunk/madman/Rpacks/ChAMP/man/champ.runCombat.Rd
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/450k.bib
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/Bumphunteroutput.png
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/CNAimage.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/CNAtext.jpg
Added  /trunk/madman/Rpacks/ChAMP/vignettes/ChAMP.Rmd
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/ChAMP.Rnw
Added  /trunk/madman/Rpacks/ChAMP/vignettes/ChAMP.bib
Added  /trunk/madman/Rpacks/ChAMP/vignettes/ChAMP.css
Added  /trunk/madman/Rpacks/ChAMP/vignettes/ChAMP.html
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/DMR.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/DMRdistributionplot.png
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/DMRoutput.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/DMRsample.pdf
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/BMIQ.jpg
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/Block-1.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/Block-2.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/Block-3.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/CNA.jpg
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/CNAGroupPlot.jpg
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/ChAMP_Pipeline.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/CpGGUI.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/DMR-1.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/DMR-2.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/DMR-3.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/DMR-4.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/EpiMod.jpg
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/Logo.jpg
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/MVP-1.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/MVP-2.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/MVP-3.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/MVP-4.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/MVP-5.png
Added  /trunk/madman/Rpacks/ChAMP/vignettes/Figure/QCGUI.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/MVP1.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/MVP2.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/MVP3.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/SVDsummary.pdf
Added  /trunk/madman/Rpacks/ChAMP/vignettes/academic-medicine.csl
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/checkBMIQ.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/densityPlot.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/failedProbes.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/figure1.pdf
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/framed.sty
Added  /trunk/madman/Rpacks/ChAMP/vignettes/header.html
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/lasso.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/logo4.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/mdsPlot.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/natbib.bst
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/probeFeatures.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/radius.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/rawSampleCluster.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/sampleSheetexample.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/studyInfo.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/studyInfo.png
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/testData_SampleSheet.csv
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/type1fit.jpg
Deleted  /trunk/madman/Rpacks/ChAMP/vignettes/type2fit.jpg
ChAMP2 upgrade.
Revision: 121614
Author: hpages
Date: 2016-10-01T08:44:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/AtlasRDF/DESCRIPTION
set Simon Jupp <jupp@ebi.ac.uk> as new maintainer
Revision: 121612
Author: s.hochreiter
Date: 2016-10-01T07:40:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/hapFabia/DESCRIPTION
Modified  /trunk/madman/Rpacks/hapFabia/inst/CITATION
citation corrected
Revision: 121609
Author: s.hochreiter
Date: 2016-10-01T07:25:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/fabia/DESCRIPTION
Modified  /trunk/madman/Rpacks/fabia/inst/CITATION
citation corrected
Revision: 121607
Author: e.garg
Date: 2016-09-30T20:12:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/sights/DESCRIPTION
Modified  /trunk/madman/Rpacks/sights/vignettes/sights.Rmd
Added transparency to plotScatter examples in vignettes/sights.Rmd; bumped version in DESCRIPTION
Revision: 121603
Author: t.silva
Date: 2016-09-30T19:48:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/methylation.R
fixing namespce
Revision: 121602
Author: t.silva
Date: 2016-09-30T19:48:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/NAMESPACE
fixing namespce
Revision: 121601
Author: t.rayner
Date: 2016-09-30T19:37:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChromHeatMap/DESCRIPTION
Bumped version number.
Revision: 121600
Author: l.gatto
Date: 2016-09-30T19:02:25+00:00
Paths:
Added  /trunk/madman/Rpacks/MSnbase/.Rbuildignore
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Modified  /trunk/madman/Rpacks/MSnbase/R/DataClasses.R
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-MSnExp.R
Modified  /trunk/madman/Rpacks/MSnbase/R/readMSData.R
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnExp-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/Spectrum2-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MSnExp.R
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_Spectrum.R
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/benchmarking.Rmd
Merge branch 'master' into devel

* master:
  Added isolationWindow,MSnExp method
  MS3 support
  simplify SSD vs HDD comparison
  Update the benchmarking vignette.
  Add comparison SSD vs HDD to benchmarking vignette
  ignore makefile and travis when building
  new gh devel version

From: Laurent <lg390@cam.ac.uk>
Revision: 121599
Author: r.thompson
Date: 2016-09-30T18:41:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/HELP/DESCRIPTION
Modified  /trunk/madman/Rpacks/HELP/R/readPairs.R
fixed error in assayDataElement update command
Revision: 121598
Author: l.collado-torres
Date: 2016-09-30T18:38:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/R/getTotalMapped.R
Modified  /trunk/madman/Rpacks/derfinder/R/loadCoverage.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_data.R
Add test for getTotalMapped()
Revision: 121597
Author: l.collado-torres
Date: 2016-09-30T18:38:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/vignettes/derfinder-users-guide.Rmd
Fixed a typo
Revision: 121595
Author: d.duverle
Date: 2016-09-30T18:19:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/cellTree/DESCRIPTION
Added  /trunk/madman/Rpacks/cellTree/inst/CITATION
Updating citation and bumping version up
Revision: 121594
Author: n.clark
Date: 2016-09-30T17:26:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/GRmetrics/DESCRIPTION
Modified  /trunk/madman/Rpacks/GRmetrics/vignettes/GRmetrics-vignette.Rmd
Fixing vignette build error. Adding definitions of metrics.

From: Nicholas Clark <clarkno@mail.uc.edu>
Revision: 121592
Author: r.castelo
Date: 2016-09-30T15:46:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/methods-MafDb2.R
Updated MafDb search by rs ID

From: Robert Castelo <robert.castelo@upf.edu>
Revision: 121589
Author: k.mezhoud
Date: 2016-09-30T14:43:55+00:00
Paths:
Added  /trunk/madman/Rpacks/bioCancer/.gitignore
Modified  /trunk/madman/Rpacks/bioCancer/DESCRIPTION
Modified  /trunk/madman/Rpacks/bioCancer/NEWS
Added  /trunk/madman/Rpacks/bioCancer/bioCancer.Rproj
Modified  /trunk/madman/Rpacks/bioCancer/inst/base/global.R
Modified  /trunk/madman/Rpacks/bioCancer/inst/bioCancer/ui.R
rm 'id=' from navbarMenu - needed for shiny update

From: kmezhoud <kmezhoud@gmail.com>
Revision: 121587
Author: t.sandmann
Date: 2016-09-30T14:32:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/gCMAP/DESCRIPTION
Modified  /trunk/madman/Rpacks/gCMAP/R/camera_score-methods.R
fixed typo
Revision: 121586
Author: j.cairns
Date: 2016-09-30T14:24:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/Chicago/DESCRIPTION
Modified  /trunk/madman/Rpacks/Chicago/R/chicago.R
Update to version 1.1.6 (data.table unique() now uses by=key() argument)
Revision: 121584
Author: g.brown
Date: 2016-09-30T13:34:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GreyListChIP/DESCRIPTION
Modified  /trunk/madman/Rpacks/GreyListChIP/NAMESPACE
Fixed bug in imports: added 'assays' from SummarizedExperiment
Revision: 121581
Author: m.dunning
Date: 2016-09-30T12:54:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/beadarray/DESCRIPTION
version number bump
Revision: 121580
Author: m.dunning
Date: 2016-09-30T12:37:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/beadarray/R/ExpressionSetIlluminaNormalisation.R
Re-do neqc normalisation. seems that removing NA is not needed any more?
Revision: 121578
Author: s.wieczorek
Date: 2016-09-30T12:30:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/Prostar/DESCRIPTION
Modified  /trunk/madman/Rpacks/Prostar/NEWS
Deleted  /trunk/madman/Rpacks/Prostar/inst/ProstarApp/report.Rmd
Modified  /trunk/madman/Rpacks/Prostar/inst/ProstarApp/server.R
Modified  /trunk/madman/Rpacks/Prostar/inst/ProstarApp/ui.R
Modified  /trunk/madman/Rpacks/Prostar/inst/doc/Prostar_Tutorial.pdf
Modified  /trunk/madman/Rpacks/Prostar/inst/doc/Prostar_UserManual.pdf
Modified  /trunk/madman/Rpacks/Prostar/vignettes/Prostar_UserManual.Rnw
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/Prostar_UserManual.pdf
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/Rcode.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/SessionLog.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/accueil.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/agregation1.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/agregation2.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/anaDiff1.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/anaDiff2.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/anaDiff3.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/anaDiff4.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/arbre.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/convert_convert.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/convert_dataID.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/convert_exp_featdata.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/convert_sampledata.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/convert_selectfile.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/defaultProstar1.png
Added  /trunk/madman/Rpacks/Prostar/vignettes/images/demoMode.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_History.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_boxplot.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_corrmatrix.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_density.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_fdata.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_heatmap.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_missValues.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_pdata.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_quantiData.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_varDist.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/desc_violinplot.png
Added  /trunk/madman/Rpacks/Prostar/vignettes/images/export.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/filter.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/filter1.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/filter2.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/filter3.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/imputation.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/logSession.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/normalisation.png
Modified  /trunk/madman/Rpacks/Prostar/vignettes/images/open_msnset.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/tableau_pval_logFC.png
Deleted  /trunk/madman/Rpacks/Prostar/vignettes/images/volcanoplot.png
Version 1.5 11
Revision: 121577
Author: m.dunning
Date: 2016-09-30T11:06:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/beadarray/R/expressionSetIllumina_channel.R
Modified  /trunk/madman/Rpacks/beadarray/R/zzz.R
Remove package startup message (no longer need to tell people that beadarray has changed)

In channel subsetting, rename new matrices prior to creating new ExpressionSetIllumina object
Revision: 121572
Author: a.wachter
Date: 2016-09-30T07:20:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/pwOmics/DESCRIPTION
Modified  /trunk/madman/Rpacks/pwOmics/R/pwOmics_read_data.R
chea database example
Revision: 121568
Author: m.jiang
Date: 2016-09-29T22:06:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
bump
Revision: 121567
Author: m.jiang
Date: 2016-09-29T22:06:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSet_Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/tests/testthat/GatingSet-testSuite.R
set colnames correctly for other.markers when swap=TRUE
Revision: 121566
Author: c.lareau
Date: 2016-09-29T21:33:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/diffloop/DESCRIPTION
Modified  /trunk/madman/Rpacks/diffloop/NAMESPACE
Modified  /trunk/madman/Rpacks/diffloop/R/annotation.R
Modified  /trunk/madman/Rpacks/diffloop/R/assoc.R
Modified  /trunk/madman/Rpacks/diffloop/R/diffloop-class.R
Modified  /trunk/madman/Rpacks/diffloop/R/pipeline_io.R
Modified  /trunk/madman/Rpacks/diffloop/R/plotting.R
Modified  /trunk/madman/Rpacks/diffloop/README.md
Modified  /trunk/madman/Rpacks/diffloop/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/featureTest.Rd
Added  /trunk/madman/Rpacks/diffloop/man/loopAssoc.Rd
Added  /trunk/madman/Rpacks/diffloop/man/loopDistancePlot.Rd
Deleted  /trunk/madman/Rpacks/diffloop/man/loopFit.Rd
Deleted  /trunk/madman/Rpacks/diffloop/man/loopTest.Rd
Deleted  /trunk/madman/Rpacks/diffloop/man/loopfit-class.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/manyLoopPlots.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/plotTopLoops.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/quickAssoc.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/quickAssocVoom.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/slidingWindowTest.Rd
Modified  /trunk/madman/Rpacks/diffloop/man/topLoops.Rd
Modified  /trunk/madman/Rpacks/diffloop/vignettes/diffloop.Rmd
Deleted  /trunk/madman/Rpacks/diffloop/vignettes/diffloop.html
vignette refresh; consolidate association methods; added functions for QC viewing

From: caleblareau <caleblareau@g.harvard.edu>
Revision: 121565
Author: v.kiselev
Date: 2016-09-29T20:58:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/SC3/DESCRIPTION
bump version
Revision: 121564
Author: v.kiselev
Date: 2016-09-29T20:57:04+00:00
Paths:
Added  /trunk/madman/Rpacks/SC3/src/Makevars
Added  /trunk/madman/Rpacks/SC3/src/Makevars.win
add Makevars
Revision: 121563
Author: m.malek
Date: 2016-09-29T19:21:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowDensity/NAMESPACE
Added SubFrame function to be exported as well
Revision: 121562
Author: r.stark
Date: 2016-09-29T16:13:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/DiffBind/R/DBA.R
Modified  /trunk/madman/Rpacks/DiffBind/R/analyze.R
Modified  /trunk/madman/Rpacks/DiffBind/R/core.R
Modified  /trunk/madman/Rpacks/DiffBind/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/DiffBind/man/dba.plotMA.Rd
Modified  /trunk/madman/Rpacks/DiffBind/man/dba.plotPCA.Rd
change formComp to components
Revision: 121561
Author: p.bellot
Date: 2016-09-29T15:39:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/netbenchmark/DESCRIPTION
Modified  /trunk/madman/Rpacks/netbenchmark/R/netbenchmark.R
- Solving a bug for saving the inferred networks
Revision: 121560
Author: t.silva
Date: 2016-09-29T15:27:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/DESCRIPTION
version bump
Revision: 121557
Author: p.bellot
Date: 2016-09-29T15:10:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/netbenchmark/DESCRIPTION
- updating version numbering
Revision: 121556
Author: p.bellot
Date: 2016-09-29T15:07:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/netbenchmark/NAMESPACE
Modified  /trunk/madman/Rpacks/netbenchmark/R/RcppExports.R
Modified  /trunk/madman/Rpacks/netbenchmark/R/netbenchmark.R
Modified  /trunk/madman/Rpacks/netbenchmark/man/netbenchmark.Rd
Modified  /trunk/madman/Rpacks/netbenchmark/src/RcppExports.cpp
- Adding option to save inferred networks
Revision: 121555
Author: g.tan
Date: 2016-09-29T14:58:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/TFBSTools/DESCRIPTION
Added  /trunk/madman/Rpacks/TFBSTools/inst/extdata/MA0001.1.pfm
Added  /trunk/madman/Rpacks/TFBSTools/inst/extdata/pfm_all_example.txt
Added  /trunk/madman/Rpacks/TFBSTools/man/readJASPARMatrix.Rd
version 1.11.8


Add the documentation
Revision: 121554
Author: m.kosinski
Date: 2016-09-29T14:21:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/RTCGA/DESCRIPTION
Modified  /trunk/madman/Rpacks/RTCGA/R/mutationsTCGA.R
Modified  /trunk/madman/Rpacks/RTCGA/RTCGA.Rproj
Modified  /trunk/madman/Rpacks/RTCGA/man/mutationsTCGA.Rd
updates in desc to avoid bioccheck warnings
Revision: 121553
Author: r.valieris
Date: 2016-09-29T14:20:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/signeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/signeR/src/gibbs_2.cpp
use rgamma instead of randg

From: rvalieris <rvalieris@users.noreply.github.com>
Revision: 121551
Author: l.collado-torres
Date: 2016-09-29T14:09:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/R/findRegions.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_findRegions.R
v1.7.13 -- provide a better error message with findRegions() when position is all FALSE
Revision: 121547
Author: jmacdon
Date: 2016-09-29T13:04:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/script/makeTxDbs.R
modify TxDb packages for release
Revision: 121546
Author: e.willighagen
Date: 2016-09-29T12:54:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/BridgeDbR/DESCRIPTION
Bumped version
Revision: 121544
Author: a.rodriguez-martinez
Date: 2016-09-29T10:31:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/MetaboSignal
Modified  /trunk/madman/Rpacks/MetaboSignal/DESCRIPTION
Modified  /trunk/madman/Rpacks/MetaboSignal/R/signaling_matrix.R
update function from hpar
Revision: 121542
Author: sdavis2
Date: 2016-09-29T10:22:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/README.md
Merge branch 'master' of github.com:seandavi/GEOquery

From: Sean Davis <seandavi@gmail.com>
Revision: 121541
Author: sdavis2
Date: 2016-09-29T10:11:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/DESCRIPTION
Version bump

From: Sean Davis <seandavi@gmail.com>
Revision: 121540
Author: sdavis2
Date: 2016-09-29T10:11:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/README.md
Just adding codecov badge

From: Sean Davis <seandavi@gmail.com>
Revision: 121539
Author: sdavis2
Date: 2016-09-29T10:11:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/R/getGEOSuppFiles.R
Modified  /trunk/madman/Rpacks/GEOquery/R/getGEOfile.R
Modified  /trunk/madman/Rpacks/GEOquery/R/parseGEO.R
http -> https

From: Alexey Sergushichev <alsergbox@gmail.com>
Revision: 121538
Author: sdavis2
Date: 2016-09-29T10:11:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.travis.yml
travis needs sudo

From: Sean Davis <seandavi@gmail.com>
Revision: 121537
Author: sdavis2
Date: 2016-09-29T10:11:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/.travis.yml
trying new travis build config

From: Sean Davis <seandavi@gmail.com>
Revision: 121536
Author: sdavis2
Date: 2016-09-29T10:11:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/GEOquery/R/getGEOSuppFiles.R
Modified  /trunk/madman/Rpacks/GEOquery/R/getGEOfile.R
Modified  /trunk/madman/Rpacks/GEOquery/R/parseGEO.R
using http protocol instead of ftp

From: Alexey Sergushichev <alsergbox@gmail.com>
Revision: 121532
Author: l.gatto
Date: 2016-09-29T09:03:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Modified  /trunk/madman/Rpacks/mzR/NEWS
Modified  /trunk/madman/Rpacks/mzR/src/Makevars.win
Merge branch 'master' into devel

* master:
  bump version
  compiles on windows, but does not load yet
  update makevars.win

From: Laurent <lg390@cam.ac.uk>
Revision: 121531
Author: s.vosse
Date: 2016-09-29T08:33:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/CGHcall/DESCRIPTION
Modified  /trunk/madman/Rpacks/CGHcall/R/CGHcall.R
Modified  /trunk/madman/Rpacks/CGHcall/man/CGHcall-package.Rd
Repaired a bug
Revision: 121529
Author: whuber
Date: 2016-09-29T08:11:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/vsn/DESCRIPTION
Modified  /trunk/madman/Rpacks/vsn/vignettes/vsn.Rnw
Fixed a consistency check in the vignette that had started to fail due to changes in the Dependencies.

Revision: 121527
Author: hpages
Date: 2016-09-29T07:37:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromUCSC.R
Update name of UCSC track associated to the knownGene table from "GENCODE v22"
to "GENCODE v24".
Revision: 121525
Author: g.yu
Date: 2016-09-29T06:36:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/ReactomePA/DESCRIPTION
Modified  /trunk/madman/Rpacks/ReactomePA/README.md
Modified  /trunk/madman/Rpacks/ReactomePA/vignettes/ReactomePA.Rmd
as.data.frame
Revision: 121523
Author: g.yu
Date: 2016-09-29T05:55:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/geom_cladelabel.R
Modified  /trunk/madman/Rpacks/ggtree/R/geom_point.R
Modified  /trunk/madman/Rpacks/ggtree/R/geom_text.R
Modified  /trunk/madman/Rpacks/ggtree/R/geom_tree.R
Modified  /trunk/madman/Rpacks/ggtree/README.md
add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
Revision: 121522
Author: v.obenchain
Date: 2016-09-29T03:29:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/script/makeTxDbs.R
specify which TxDb packages will be built for Bioconductor 3.4
Revision: 121521
Author: rscharpf
Date: 2016-09-29T01:13:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPchip/DESCRIPTION
Modified  /trunk/madman/Rpacks/SNPchip/vignettes/PlottingIdiograms.Rnw
Package maintained for historical reasons

no longer actively developed

From: Robert Scharpf <rscharpf@jhu.edu>
Revision: 121520
Author: rscharpf
Date: 2016-09-29T01:13:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPchip/DESCRIPTION
Modified  /trunk/madman/Rpacks/SNPchip/inst/unitTests/test_xyplot.R
Modified  /trunk/madman/Rpacks/SNPchip/man/xypanel.Rd
Modified  /trunk/madman/Rpacks/SNPchip/man/xyplot.Rd
Modified  /trunk/madman/Rpacks/SNPchip/man/xyplotLrrBaf.Rd
Replace hmm with hmm2

From: Robert Scharpf <rscharpf@jhu.edu>
Revision: 121519
Author: t.silva
Date: 2016-09-28T23:43:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/man/GDCdownload.Rd
verifying input in survival
Revision: 121518
Author: t.silva
Date: 2016-09-28T23:43:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGADownload.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/methylation.R
verifying input in survival
Revision: 121517
Author: m.lawrence
Date: 2016-09-28T21:41:13+00:00
Paths:
Added  /trunk/madman/Rpacks/rsbml/INSTALL
add INSTALL file with Windows build instructions

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: