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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)
Revision: 124732
Author: t.gorrie-stone
Date: 2016-12-02T09:34:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/bigmelon/DESCRIPTION
Modified  /trunk/madman/Rpacks/bigmelon/R/gds2mlumi.R
Modified  /trunk/madman/Rpacks/bigmelon/vignettes/bigmelon.Rnw
Fixing error in gds2mset by minfi update and updating vignette to have quick-start
Revision: 124730
Author: p.angerer
Date: 2016-12-02T08:29:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/R/diffusionmap.r
Modified  /trunk/madman/Rpacks/destiny/tests/testthat/test_distances.r
removed that offending factor 2 again
Revision: 124728
Author: p.angerer
Date: 2016-12-02T08:29:33+00:00
Paths:
Deleted  /trunk/madman/Rpacks/destiny/inst/doc/mmc4.xls
Deleted  /trunk/madman/Rpacks/destiny/inst/doc/mmc6.xls
Added  /trunk/madman/Rpacks/destiny/vignettes/mmc4.xls
Added  /trunk/madman/Rpacks/destiny/vignettes/mmc6.xls
no need to install xls files
Revision: 124727
Author: hpages
Date: 2016-12-02T06:28:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/NAMESPACE
don't import "ifelse" method from S4Vectors: there is no such method
Revision: 124726
Author: v.obenchain
Date: 2016-12-02T02:51:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHub/NAMESPACE
move utils to 'depends' for read.csv() access by packages
depending on ExperimentHub
Revision: 124725
Author: h.luan
Date: 2016-12-02T01:00:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/statTarget/DESCRIPTION
H_luan_grammar
Revision: 124724
Author: h.luan
Date: 2016-12-02T00:59:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/statTarget/R/statTarget-package.R
H_luan
Revision: 124719
Author: m.smith
Date: 2016-12-01T23:46:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/IONiseR/NEWS
Updated news file
Revision: 124718
Author: hpages
Date: 2016-12-01T22:13:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/TODO
test
Revision: 124717
Author: m.love
Date: 2016-12-01T18:50:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_outlier.R
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rmd
tweaking tests
Revision: 124713
Author: m.jiang
Date: 2016-12-01T18:34:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/DESCRIPTION
bump
Revision: 124712
Author: m.jiang
Date: 2016-12-01T18:34:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/src/convertRawBytes.cpp
Modified  /trunk/madman/Rpacks/flowCore/src/fcsTextParse.cpp
temporarily switch from Rcpp::stop to range_error due to a bug in Rcpp 0.12.8.  RcppCore/Rcpp#596
Revision: 124710
Author: l.collado-torres
Date: 2016-12-01T18:25:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/recount/DESCRIPTION
v1.1.10 -- add DataImport biocview
Revision: 124708
Author: j.ou
Date: 2016-12-01T17:01:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/trackViewer/DESCRIPTION
Modified  /trunk/madman/Rpacks/trackViewer/NEWS
Modified  /trunk/madman/Rpacks/trackViewer/R/plotTrack.R
fix a bug when tracks has multiple max values.
Revision: 124706
Author: m.ramos
Date: 2016-12-01T16:33:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GRangesList-class.R
add list to GRangesList coercion and coerce at constructor
Revision: 124705
Author: a.oles
Date: 2016-12-01T15:16:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/pdf_document2.R
Modified  /trunk/madman/Rpacks/BiocStyle/inst/resources/tex/Bioconductor2.sty
version 2.3.18
- 'pdf_document2()': use 'bookdown::pdf_book'
- fix to retain spaces in '\texttt'

From: aoles <andrzej.oles@gmail.com>
Revision: 124704
Author: s.grote
Date: 2016-12-01T15:13:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/ABAEnrichment/R/aba_enrich.R
Modified  /trunk/madman/Rpacks/ABAEnrichment/R/rearrange_output.R
Modified  /trunk/madman/Rpacks/ABAEnrichment/src/hyper_categorytest.cc
Modified  /trunk/madman/Rpacks/ABAEnrichment/src/hyper_randset.cc
Modified  /trunk/madman/Rpacks/ABAEnrichment/src/wilcox_categorytest.cc
Minor changes in sorting of output and prints to screen.
Revision: 124703
Author: j.hon
Date: 2016-12-01T12:40:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/pqsfinder/NEWS
Version bump. News update.
Revision: 124702
Author: j.hon
Date: 2016-12-01T12:39:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/R/PQSViews-class.R
Modified  /trunk/madman/Rpacks/pqsfinder/R/RcppExports.R
Modified  /trunk/madman/Rpacks/pqsfinder/man/PQSViews.Rd
Modified  /trunk/madman/Rpacks/pqsfinder/man/pqsfinder.Rd
Added  /trunk/madman/Rpacks/pqsfinder/src/features.h
Modified  /trunk/madman/Rpacks/pqsfinder/src/pqs_cache.h
Modified  /trunk/madman/Rpacks/pqsfinder/src/pqs_storage.h
Modified  /trunk/madman/Rpacks/pqsfinder/src/pqsfinder.cpp
Modified  /trunk/madman/Rpacks/pqsfinder/src/results.h
Added new metadata for each PQS describing number of tetrads, bulges, mismatches and loop lengths. It is accessible by elementMetadata function. Also slightly improved mismatch absorbance for the first and the last G-run.
Revision: 124701
Author: h.luan
Date: 2016-12-01T11:13:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/statTarget/R/plsda_stat.R
H_luan_tVIP
Revision: 124697
Author: g.zararsiz
Date: 2016-12-01T09:48:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLSeq/DESCRIPTION
devel version moved to 1.15.2

From: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Revision: 124696
Author: g.zararsiz
Date: 2016-12-01T09:48:48+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.R
Deleted  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.Rnw
Deleted  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.pdf
Modified  /trunk/madman/Rpacks/MLSeq/vignettes/MLSeq.Rnw
Revert "Revert "vignette is updated - minor fixes""

This reverts commit d4f1c4853335037f69e2ca2f35fd0befeeafdabe.

From: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Revision: 124695
Author: g.zararsiz
Date: 2016-12-01T09:48:35+00:00
Paths:
Added  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.R
Added  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.Rnw
Added  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.pdf
Modified  /trunk/madman/Rpacks/MLSeq/vignettes/MLSeq.Rnw
Revert "vignette is updated - minor fixes"

This reverts commit 21f96500608a9b0fa673d5f214d56bc607441b8c.

From: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Revision: 124694
Author: g.zararsiz
Date: 2016-12-01T09:48:23+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.R
Deleted  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.Rnw
Deleted  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.pdf
Modified  /trunk/madman/Rpacks/MLSeq/vignettes/MLSeq.Rnw
vignette is updated - minor fixes

From: Dincer GOKSULUK <dincer.goksuluk@gmail.com>
Revision: 124691
Author: h.luan
Date: 2016-12-01T09:16:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/statTarget/R/statAnalysis.R
H_luan
Revision: 124690
Author: h.luan
Date: 2016-12-01T09:15:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/statTarget/R/shiftCor_v2.R
H_luan
Revision: 124689
Author: hpages
Date: 2016-12-01T07:41:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/OverlapEncodings-class.R
Modified  /trunk/madman/Rpacks/GenomicAlignments/man/OverlapEncodings-class.Rd
- Add low-level encoding utility encodingHalves().
- Minor tweaks to low-level encoding utilities Lencoding(), Rencoding(),
  Lnjunc(), Rnjunc(), and njunc(). All of them now are based on
  encodingHalves().
Revision: 124688
Author: m.riester
Date: 2016-12-01T04:52:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Restructured vignette.
Revision: 124687
Author: m.riester
Date: 2016-12-01T04:26:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
More vignette cleanups.
Revision: 124686
Author: s.manimaran
Date: 2016-12-01T04:20:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/PathoStat/DESCRIPTION
Modified  /trunk/madman/Rpacks/PathoStat/NAMESPACE
Modified  /trunk/madman/Rpacks/PathoStat/R/pathoStat.R
Modified  /trunk/madman/Rpacks/PathoStat/inst/shiny/PathoStat/server.R
Modified  /trunk/madman/Rpacks/PathoStat/inst/shiny/PathoStat/ui.R
Adding DESeq2 differential abundance analysis tab and fixing normalization for EdgeR. Calling phyloseq distance function explicitly to avoid conflict.
Revision: 124684
Author: m.riester
Date: 2016-12-01T03:45:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
More vignette cleanups.
Revision: 124683
Author: m.riester
Date: 2016-12-01T01:52:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
More minor vignette tweaks.
Revision: 124682
Author: m.riester
Date: 2016-12-01T00:32:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/Coverage.R
Forgot to add --force to second step.
Revision: 124681
Author: m.riester
Date: 2016-12-01T00:29:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/Coverage.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/PureCN.R
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Updated command line scripts for recent PureCN changes.

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