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: 124834
Author: t.smith
Date: 2016-12-05T19:59:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowPloidy/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowPloidy/NAMESPACE
Modified  /trunk/madman/Rpacks/flowPloidy/R/FlowHist.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/flowAnalysis.R
Added  /trunk/madman/Rpacks/flowPloidy/R/flowGate.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/models.R
Modified  /trunk/madman/Rpacks/flowPloidy/R/shiny.R
Modified  /trunk/madman/Rpacks/flowPloidy/TODO.org
Modified  /trunk/madman/Rpacks/flowPloidy/inst/NEWS
Modified  /trunk/madman/Rpacks/flowPloidy/man/FlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/browseFlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/fhAnalyze.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/findPeaks.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/gauss.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/pickInit.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/plot.FlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/plotFH.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/setBins.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/tabulateFlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/updateFlowHist.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/man/viewFlowChannels.Rd
Modified  /trunk/madman/Rpacks/flowPloidy/test-script.R
Added  /trunk/madman/Rpacks/flowPloidy/tests
Added  /trunk/madman/Rpacks/flowPloidy/tests/testthat
Added  /trunk/madman/Rpacks/flowPloidy/tests/testthat/testcore.R
Added  /trunk/madman/Rpacks/flowPloidy/tests/testthat/testmodels.R
Added  /trunk/madman/Rpacks/flowPloidy/tests/testthat.R
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowPloidy-overview.Rmd
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny01.png
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny02.png
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny03.png
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny04.png
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny05.png
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny06.png
Modified  /trunk/madman/Rpacks/flowPloidy/vignettes/flowShiny07.png
gating protocol implemented
Revision: 124833
Author: a.lun
Date: 2016-12-05T19:54:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/scran/DESCRIPTION
Modified  /trunk/madman/Rpacks/scran/tests/testthat/test-normalize.R
Updated normalize tests for new scater.
Revision: 124832
Author: s.white
Date: 2016-12-05T19:31:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGlincs/DESCRIPTION
add Dr Medvedovic to DESC as maintainer

From: vandersm <vandersm@mail.uc.edu>
Revision: 124831
Author: s.white
Date: 2016-12-05T19:12:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGlincs/README.md
change .png to .jpeg for overview pic

From: Shana White <vandersm@mail.uc.edu>
Revision: 124830
Author: v.obenchain
Date: 2016-12-05T18:43:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHub/man/ExperimentHub-class.Rd
clarify definition of possibleDates()
Revision: 124829
Author: d.mccarthy
Date: 2016-12-05T16:13:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/scater/R/SCESet-methods.R
Modified  /trunk/madman/Rpacks/scater/R/normalisation.R
Switched to our exprs calculation from cpm.default.

From: Aaron Lun <alun@wehi.edu.au>
Revision: 124828
Author: d.mccarthy
Date: 2016-12-05T16:13:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/scater/R/calculate-expression.R
Standardized nexprs arguments.

From: Aaron Lun <alun@wehi.edu.au>
Revision: 124827
Author: d.mccarthy
Date: 2016-12-05T16:13:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/scater/R/calculate-expression.R
Modified  /trunk/madman/Rpacks/scater/R/normalisation.R
Modified  /trunk/madman/Rpacks/scater/R/qc.R
Added  /trunk/madman/Rpacks/scater/R/utils.R
Moved functions into more appropriate places.
Added calcAverage function for normalized average counts.

From: Aaron Lun <alun@wehi.edu.au>
Revision: 124826
Author: d.mccarthy
Date: 2016-12-05T16:13:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/scater/R/qc.R
Bug fix.

From: Aaron Lun <alun@wehi.edu.au>
Revision: 124825
Author: d.mccarthy
Date: 2016-12-05T16:13:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/scater/R/normalisation.R
Modified  /trunk/madman/Rpacks/scater/R/qc.R
Deleted  /trunk/madman/Rpacks/scater/src/calc_cpm.cpp
Added  /trunk/madman/Rpacks/scater/src/calc_exprs.cpp
Modified  /trunk/madman/Rpacks/scater/src/init.cpp
Modified  /trunk/madman/Rpacks/scater/src/scater.h
Modified  /trunk/madman/Rpacks/scater/src/utils.cpp
Compute size factor-corrected normalized counts.
Refactored subsetting code for easier use.

From: Aaron Lun <alun@wehi.edu.au>
Revision: 124824
Author: m.lawrence
Date: 2016-12-05T15:41:25+00:00
Paths:
Added  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_split.R
add a regression test for the as.factor2() case
Revision: 124823
Author: m.lawrence
Date: 2016-12-05T15:35:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/extractList.R
fix as.factor2() for non-character input
Revision: 124822
Author: m.love
Date: 2016-12-05T14:32:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_outlier.R
fix test bug
Revision: 124821
Author: m.love
Date: 2016-12-05T14:27:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/tximport/DESCRIPTION
Added  /trunk/madman/Rpacks/tximport/tests/testthat/test_no_tx2gene.R
Added  /trunk/madman/Rpacks/tximport/tests/testthat/test_rsem.R
adding missing tests
Revision: 124820
Author: v.obenchain
Date: 2016-12-05T14:18:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/GenomicScoresResource-class.R
add back deleted commas to .get1,GenomicScoresResource-method
Revision: 124819
Author: j.hon
Date: 2016-12-05T13:14:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/vignettes
Ignore vignette outputs.
Revision: 124818
Author: j.hon
Date: 2016-12-05T13:14:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/DESCRIPTION
Version bump.
Revision: 124817
Author: j.hon
Date: 2016-12-05T13:13:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/R/RcppExports.R
Modified  /trunk/madman/Rpacks/pqsfinder/man/pqsfinder.Rd
Modified  /trunk/madman/Rpacks/pqsfinder/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/pqsfinder/src/pqsfinder.cpp
Added bulge_len_factor and bulge_len_exponent options.
Revision: 124816
Author: j.hon
Date: 2016-12-05T12:43:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/DESCRIPTION
Version bump.
Revision: 124815
Author: j.hon
Date: 2016-12-05T12:42:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/R/RcppExports.R
Modified  /trunk/madman/Rpacks/pqsfinder/man/pqsfinder.Rd
Modified  /trunk/madman/Rpacks/pqsfinder/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/pqsfinder/src/pqsfinder.cpp
Added edge_mismatch_penalty option.
Revision: 124813
Author: m.lienhard
Date: 2016-12-05T11:03:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/qsea/inst/CITATION
citation updated final
Revision: 124811
Author: m.lienhard
Date: 2016-12-05T10:59:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/qsea/inst/CITATION
citation updated final
Revision: 124809
Author: m.lienhard
Date: 2016-12-05T10:34:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/qsea/inst/CITATION
citation updated4
Revision: 124807
Author: m.lienhard
Date: 2016-12-05T10:24:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/qsea/inst/CITATION
citation updated3
Revision: 124804
Author: m.lienhard
Date: 2016-12-05T09:29:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/qsea/DESCRIPTION
Modified  /trunk/madman/Rpacks/qsea/NAMESPACE
Modified  /trunk/madman/Rpacks/qsea/NEWS
Modified  /trunk/madman/Rpacks/qsea/R/qsea.normalize.R
Added  /trunk/madman/Rpacks/qsea/inst/CITATION
citation updated
Revision: 124802
Author: s.su
Date: 2016-12-05T06:30:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/Glimma/DESCRIPTION
Modified  /trunk/madman/Rpacks/Glimma/NAMESPACE
Modified  /trunk/madman/Rpacks/Glimma/R/dataDoc.R
Modified  /trunk/madman/Rpacks/Glimma/R/glBar.R
Modified  /trunk/madman/Rpacks/Glimma/R/glInputs.R
Modified  /trunk/madman/Rpacks/Glimma/R/glMDPlot.R
Modified  /trunk/madman/Rpacks/Glimma/R/glMDSPlot.R
Modified  /trunk/madman/Rpacks/Glimma/R/glScatter.R
Modified  /trunk/madman/Rpacks/Glimma/R/glXYPlot.R
Modified  /trunk/madman/Rpacks/Glimma/R/glimma.R
Modified  /trunk/madman/Rpacks/Glimma/R/gltablink.R
Modified  /trunk/madman/Rpacks/Glimma/R/jsHelper.R
Modified  /trunk/madman/Rpacks/Glimma/R/jsonConvert.R
Modified  /trunk/madman/Rpacks/Glimma/R/plotWithTable.R
Modified  /trunk/madman/Rpacks/Glimma/R/utilities.R
Modified  /trunk/madman/Rpacks/Glimma/inst/css/glimma.min.css
Modified  /trunk/madman/Rpacks/Glimma/inst/js/glimma.min.js
Modified  /trunk/madman/Rpacks/Glimma/man/as.hexcol.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glMDPlot.DESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glMDPlot.DESeqResults.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glMDPlot.DGEExact.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glMDPlot.DGELRT.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glMDPlot.MArrayLM.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glMDPlot.default.Rd
Modified  /trunk/madman/Rpacks/Glimma/man/glXYPlot.Rd
Modified  /trunk/madman/Rpacks/Glimma/svn-commit.tmp~
Modified  /trunk/madman/Rpacks/Glimma/vignettes/Glimma.Rnw
Version Update
Revision: 124801
Author: z.yang
Date: 2016-12-05T06:11:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/FEM/DESCRIPTION
Modified  /trunk/madman/Rpacks/FEM/man/DoFEMbi.Rd
I updated FEM.
Revision: 124798
Author: v.obenchain
Date: 2016-12-05T01:47:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHubData/vignettes/ExperimentHubData.Rmd
update vignette to suggest ExperimentHub::createHubAccessors()
Revision: 124797
Author: v.obenchain
Date: 2016-12-05T01:40:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHub/NAMESPACE
Modified  /trunk/madman/Rpacks/ExperimentHub/R/utilities.R
Modified  /trunk/madman/Rpacks/ExperimentHub/man/ExperimentHub-class.Rd
add createHubAccessors() for function generation in contributed pacakges
Revision: 124795
Author: p.hickey
Date: 2016-12-04T21:35:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicTuples/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicTuples/R/GTuples-comparison.R
Fix failing tests
Revision: 124794
Author: m.smith
Date: 2016-12-04T21:07:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/IONiseR/DESCRIPTION
Modified  /trunk/madman/Rpacks/IONiseR/NAMESPACE
Modified  /trunk/madman/Rpacks/IONiseR/R/fast5Readers.R
Modified  /trunk/madman/Rpacks/IONiseR/R/plotting_layout.R
Modified  /trunk/madman/Rpacks/IONiseR/R/plotting_summaryStats.R
Modified  /trunk/madman/Rpacks/IONiseR/R/readSummary.R
Added some missing imports to NAMESPACE
Revision: 124793
Author: l.urban
Date: 2016-12-04T18:11:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/R/plot.ord.R
Merge branch 'master' into devel

* master:
  corrected error and changed version number
  adapted man page of plo.ord
  anged plot ord
  ange rangx and rangey
  change plot function

From: LaraUrban <lara.urban@gmx.de>
Revision: 124792
Author: l.urban
Date: 2016-12-04T18:11:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/vignettes/covRNA.Rmd
update vignette

From: LaraUrban <lara.urban@gmx.de>
Revision: 124791
Author: l.urban
Date: 2016-12-04T18:11:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/README.md
check file

From: LaraUrban <lara.urban@gmx.de>
Revision: 124790
Author: l.urban
Date: 2016-12-04T18:11:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/R/vis.R
improve plotting function

From: LaraUrban <lara.urban@gmx.de>
Revision: 124789
Author: l.urban
Date: 2016-12-04T18:11:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/R/stat.R
add statistical tests

From: LaraUrban <lara.urban@gmx.de>
Revision: 124788
Author: l.urban
Date: 2016-12-04T18:11:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/R/plot.stat.R
improve plotting function

From: LaraUrban <lara.urban@gmx.de>
Revision: 124787
Author: l.urban
Date: 2016-12-04T18:11:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/R/plot.ord.R
improve plotting function

From: LaraUrban <lara.urban@gmx.de>
Revision: 124786
Author: l.urban
Date: 2016-12-04T18:11:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/R/ord.R
change factor handling in ord function

From: LaraUrban <lara.urban@gmx.de>
Revision: 124785
Author: l.urban
Date: 2016-12-04T18:11:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/covRNA/DESCRIPTION
change version number

From: LaraUrban <lara.urban@gmx.de>
Revision: 124781
Author: a.mayakonda
Date: 2016-12-04T14:10:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/maftools/R/clusterScore.R
Modified  /trunk/madman/Rpacks/maftools/R/domainSummary.R
Modified  /trunk/madman/Rpacks/maftools/R/mathScore.R
Modified  /trunk/madman/Rpacks/maftools/R/plotOncodriveClust.R
Modified  /trunk/madman/Rpacks/maftools/inst/NEWS
oncodrive bug fix
Revision: 124778
Author: m.riester
Date: 2016-12-04T01:32:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Fixed newly introduced bug in plotAbs, type=overview.
Revision: 124776
Author: m.riester
Date: 2016-12-03T23:52:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/NEWS
Modified  /trunk/madman/Rpacks/PureCN/R/findBestNormal.R
Modified  /trunk/madman/Rpacks/PureCN/R/setMappingBiasVcf.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/PureCN.R
Modified  /trunk/madman/Rpacks/PureCN/man/setMappingBiasVcf.Rd
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Added predictSomatic functionality to PureCN.R command line script; support for smaller panel of normals.
Revision: 124775
Author: stvjc
Date: 2016-12-03T21:22:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/collapse_multiPerm.R
speeding up distToGene
Revision: 124773
Author: k.rue-albrecht
Date: 2016-12-03T18:10:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOexpress/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOexpress/NAMESPACE
Modified  /trunk/madman/Rpacks/GOexpress/NEWS
Modified  /trunk/madman/Rpacks/GOexpress/R/post_analysis.R
Buf fix after ggplot update.
Revision: 124772
Author: a.oles
Date: 2016-12-03T15:42:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/knitr_options.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/latex2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/markdown.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/pdf_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/rmd_common.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/utils.R
version 2.3.22
- properly import bookdown, rmarkdown, and knitr

From: aoles <andrzej.oles@gmail.com>
Revision: 124771
Author: e.mathieu
Date: 2016-12-03T14:57:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneGeneInteR/DESCRIPTION
Modified  /trunk/madman/Rpacks/GeneGeneInteR/NAMESPACE
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/CCA.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/CLD.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/GATES.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/GBIGM.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/GGI.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/KCCA.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/PCA.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/PLSPM.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/minP.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/plot.GGInetwork.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/tProd.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/R/tTS.R
Modified  /trunk/madman/Rpacks/GeneGeneInteR/README.md
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/CCA.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/CLD.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/GBIGM.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/KCCA.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/PCA.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/PLSPM.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/gates.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/minP.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/plot.GGInetwork.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/tProd.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/man/tTS.test.Rd
Modified  /trunk/madman/Rpacks/GeneGeneInteR/vignettes/GenePair.Rnw
v.1.1.1
Revision: 124770
Author: mtmorgan
Date: 2016-12-03T14:57:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/CNExperiment/DESCRIPTION
Modified  /trunk/madman/Rpacks/CNExperiment/NAMESPACE
Modified  /trunk/madman/Rpacks/CNExperiment/R/CNExperiment-class.R
Modified  /trunk/madman/Rpacks/CNExperiment/tests/testthat/test_CNExperiment-class.R
assay() supports seletion by integer or character index

- assays() also propagates names
Revision: 124769
Author: stvjc
Date: 2016-12-03T14:26:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/collapse_multiPerm.R
Modified  /trunk/madman/Rpacks/gQTLstats/inst/unitTests/test_gQTLstats.R
improve d2g and its test
Revision: 124767
Author: stvjc
Date: 2016-12-03T13:44:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/inst/unitTests/test_gQTLstats.R
new unit test for distToGene
Revision: 124766
Author: a.oles
Date: 2016-12-03T13:24:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/pdf_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/R/utils.R
version 2.3.21
- check whether bookdown is installed
- remove MathJax equation number configuration from 'html_document()' (handled by bookdown)

From: aoles <andrzej.oles@gmail.com>
Revision: 124765
Author: m.love
Date: 2016-12-03T13:21:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rmd
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2_pdf.Rmd
fix soul error vignette
Revision: 124764
Author: stvjc
Date: 2016-12-03T12:50:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/collapse_multiPerm.R
fixup distToGene to use native distance for GRanges
Revision: 124762
Author: mtmorgan
Date: 2016-12-03T09:38:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GRangesList-class.R
revert r124706, add list to GRangesList coercion
Revision: 124761
Author: l.goldstein
Date: 2016-12-03T02:06:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/plots.R
Bug fix - when plotting gene models using the geneName argument, splice-site-only models caused an error
Revision: 124759
Author: stvjc
Date: 2016-12-03T01:46:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/collapse_multiPerm.R
Modified  /trunk/madman/Rpacks/gQTLstats/inst/unitTests/test_gQTLstats.R
trying to move multiperm along
Revision: 124757
Author: a.oles
Date: 2016-12-02T21:03:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_document2.R
version 2.3.20
- fixes #20

From: aoles <andrzej.oles@gmail.com>
Revision: 124756
Author: l.collado-torres
Date: 2016-12-02T20:58:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/DESCRIPTION
v1.9.4 -- require BiocStyle 2.3.20 due to https://github.com/Bioconductor/BiocStyle/issues/20
Revision: 124755
Author: l.collado-torres
Date: 2016-12-02T20:58:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/recount/DESCRIPTION
And the corresponding regionReport version
Revision: 124754
Author: l.collado-torres
Date: 2016-12-02T20:57:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/recount/DESCRIPTION
v1.1.11 -- require BiocStyle 2.3.20 due to https://github.com/Bioconductor/BiocStyle/issues/20
Revision: 124753
Author: b.afsari
Date: 2016-12-02T20:05:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSReg/NAMESPACE
Modified  /trunk/madman/Rpacks/GSReg/R/exportedFuncs.R
Modified  /trunk/madman/Rpacks/GSReg/src/kendallTauDistanceFromTemp.cc
Modified  /trunk/madman/Rpacks/GSReg/vignettes/GSReg.Rnw
Fixing bugs in the vignette.
Revision: 124752
Author: s.manimaran
Date: 2016-12-02T19:28:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/PathoStat/DESCRIPTION
Modified  /trunk/madman/Rpacks/PathoStat/R/normalization.R
Modified  /trunk/madman/Rpacks/PathoStat/inst/shiny/PathoStat/ui.R
Modified  /trunk/madman/Rpacks/PathoStat/man/coreOTUNormalize.Rd
Modified  /trunk/madman/Rpacks/PathoStat/man/coreOTUQuantile.Rd
Fixing document warning and removing MDS method in BiPlot as it is same as PCoA
Revision: 124751
Author: m.love
Date: 2016-12-02T19:22:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rmd
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2_pdf.Rmd
fix vignette
Revision: 124750
Author: v.obenchain
Date: 2016-12-02T18:58:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/GenomicScoresResource-class.R
modify Robert's .get1,GenomicScoresResource-method
Revision: 124749
Author: d.mccarthy
Date: 2016-12-02T18:17:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/scater/.gitignore
Modified  /trunk/madman/Rpacks/scater/DESCRIPTION
Modified  /trunk/madman/Rpacks/scater/R/qc.R
Modified  /trunk/madman/Rpacks/scater/man/isOutlier.Rd
Fixing version number conflict

From: davismcc <davismcc@gmail.com>
Revision: 124746
Author: r.stark
Date: 2016-12-02T17:18:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/DiffBind/DESCRIPTION
Modified  /trunk/madman/Rpacks/DiffBind/R/analyze.R
fix bug using bFlip with DBA_EDGER
Revision: 124745
Author: m.riester
Date: 2016-12-02T16:59:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/NAMESPACE
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/PureCN.R
Modified  /trunk/madman/Rpacks/PureCN/man/plotAbs.Rd
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Added overview2 plot.
Revision: 124744
Author: stvjc
Date: 2016-12-02T16:20:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/NAMESPACE
Added  /trunk/madman/Rpacks/gQTLstats/R/collapse_multiPerm.R
Modified  /trunk/madman/Rpacks/gQTLstats/R/pifdr.R
Modified  /trunk/madman/Rpacks/gQTLstats/inst/unitTests/test_gQTLstats.R
provisional commitment to use on new host, multi-perm AllAssoc starting
Revision: 124743
Author: r.valieris
Date: 2016-12-02T16:16:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/signeR/DESCRIPTION
fixed package title

From: rvalieris <rvalieris@users.noreply.github.com>
Revision: 124742
Author: a.oles
Date: 2016-12-02T14:58:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_document2.R
Added  /trunk/madman/Rpacks/BiocStyle/vignettes/AuthoringRmdVignettes.Rmd
Modified  /trunk/madman/Rpacks/BiocStyle/vignettes/LatexStyle2.Rnw
version 2.3.19
- add "Authoring R Markdown vignettes" vignette
- 'html_document()': remove periods after caption titles

From: aoles <andrzej.oles@gmail.com>
Revision: 124741
Author: mtmorgan
Date: 2016-12-02T14:50:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/CNExperiment/R/CNExperiment-class.R
Modified  /trunk/madman/Rpacks/CNExperiment/R/CNExperiment-methods.R
Modified  /trunk/madman/Rpacks/CNExperiment/man/CNExperiment-class.Rd
allow duplicate rowRanges; implement row subsetting
Revision: 124737
Author: mtmorgan
Date: 2016-12-02T14:11:03+00:00
Paths:
Deleted  /trunk/madman/Rpacks/CNExperiment/R/CNExperiment.R
delete empty file
Revision: 124735
Author: fhahne
Date: 2016-12-02T13:04:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/NAMESPACE
Modified  /trunk/madman/Rpacks/Gviz/NEWS
Modified  /trunk/madman/Rpacks/Gviz/R/AllClasses.R
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz-methods.R
Modified  /trunk/madman/Rpacks/Gviz/inst/scripts/documentation.R
Modified  /trunk/madman/Rpacks/Gviz/man
Modified  /trunk/madman/Rpacks/Gviz/man/AlignedReadTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/AlignmentsTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/AnnotationTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/BiomartGeneRegionTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/CustomTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/DataTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/DisplayPars-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/GdObject-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/GeneRegionTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/GenomeAxisTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/HighlightTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/IdeogramTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/ImageMap-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/NumericTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/OverlayTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/RangeTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/ReferenceTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/SequenceTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/StackedTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/UcscTrack.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/collapsing.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/datasets.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/exportTracks.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/grouping.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/plotTracks.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/settings.Rd
Modified  /trunk/madman/Rpacks/Gviz/vignettes
Modified  /trunk/madman/Rpacks/Gviz/vignettes/Gviz.Rnw
making the Biomart connections to non-standard genomes a bit more robust
Revision: 124734
Author: s.grote
Date: 2016-12-02T10:28:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/ABAEnrichment/R/aba_enrich.R
Fix 'Allen:Allen:'-bug from last commit (in saved expression dataset)

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: