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Revision: 119757
Author: b.callahan
Date: 2016-07-29T22:58:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/dada2/DESCRIPTION
Modified  /trunk/madman/Rpacks/dada2/NAMESPACE
Modified  /trunk/madman/Rpacks/dada2/NEWS
Modified  /trunk/madman/Rpacks/dada2/R/RcppExports.R
Modified  /trunk/madman/Rpacks/dada2/R/dada.R
Modified  /trunk/madman/Rpacks/dada2/R/misc.R
Modified  /trunk/madman/Rpacks/dada2/R/multiSample.R
Modified  /trunk/madman/Rpacks/dada2/R/plot-methods.R
Modified  /trunk/madman/Rpacks/dada2/R/taxonomy.R
Modified  /trunk/madman/Rpacks/dada2/README.md
Modified  /trunk/madman/Rpacks/dada2/build/vignette.rds
Modified  /trunk/madman/Rpacks/dada2/inst/doc/dada2-intro.html
Added  /trunk/madman/Rpacks/dada2/man/addSpecies.Rd
Added  /trunk/madman/Rpacks/dada2/man/assignSpecies.Rd
Modified  /trunk/madman/Rpacks/dada2/man/assignTaxonomy.Rd
Modified  /trunk/madman/Rpacks/dada2/man/dada.Rd
Added  /trunk/madman/Rpacks/dada2/man/makeSpeciesFasta_RDP.Rd
Added  /trunk/madman/Rpacks/dada2/man/makeSpeciesFasta_Silva.Rd
Added  /trunk/madman/Rpacks/dada2/man/mergeSequenceTables.Rd
Modified  /trunk/madman/Rpacks/dada2/man/plotQualityProfile.Rd
Modified  /trunk/madman/Rpacks/dada2/man/setDadaOpt.Rd
Added  /trunk/madman/Rpacks/dada2/src/Makevars
Modified  /trunk/madman/Rpacks/dada2/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/dada2/src/Rmain.cpp
Modified  /trunk/madman/Rpacks/dada2/src/chimera.cpp
Modified  /trunk/madman/Rpacks/dada2/src/cluster.cpp
Modified  /trunk/madman/Rpacks/dada2/src/dada.h
Modified  /trunk/madman/Rpacks/dada2/src/error.cpp
Modified  /trunk/madman/Rpacks/dada2/src/evaluate.cpp
Modified  /trunk/madman/Rpacks/dada2/src/filter.cpp
Modified  /trunk/madman/Rpacks/dada2/src/nwalign_endsfree.cpp
Modified  /trunk/madman/Rpacks/dada2/src/nwalign_vectorized.cpp
Modified  /trunk/madman/Rpacks/dada2/src/pval.cpp
1.1.3: C++11 and RcppParallel plus major functional additions
Revision: 119756
Author: l.pantano
Date: 2016-07-29T21:42:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/isomiRs/NEWS
Deleted  /trunk/madman/Rpacks/isomiRs/isomiRs.Rproj
Update news

From: Lorena Pantano <lorena.pantano@gmail.com>
Revision: 119755
Author: l.pantano
Date: 2016-07-29T21:42:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/isomiRs/R/targets.R
Improve code

From: Lorena Pantano <lorena.pantano@gmail.com>
Revision: 119754
Author: l.pantano
Date: 2016-07-29T21:42:30+00:00
Paths:
Added  /trunk/madman/Rpacks/isomiRs/data/isoExample.rda
Modified  /trunk/madman/Rpacks/isomiRs/man/isoNetwork.Rd
Improve docs

Add new data

From: Lorena Pantano <lorena.pantano@gmail.com>
Revision: 119752
Author: l.pantano
Date: 2016-07-29T21:42:16+00:00
Paths:
Added  /trunk/madman/Rpacks/isomiRs/.travis.yml
Modified  /trunk/madman/Rpacks/isomiRs/DESCRIPTION
Modified  /trunk/madman/Rpacks/isomiRs/NAMESPACE
Modified  /trunk/madman/Rpacks/isomiRs/NEWS
Modified  /trunk/madman/Rpacks/isomiRs/R/AllClasses.R
Added  /trunk/madman/Rpacks/isomiRs/R/targets.R
Merge branch 'upstream' into bioc

From: Lorena Pantano <lorena.pantano@gmail.com>
Revision: 119751
Author: d.risso
Date: 2016-07-29T21:24:31+00:00
Paths:
Added  /trunk/madman/Rpacks/clusterExperiment/.Rbuildignore
Added  /trunk/madman/Rpacks/clusterExperiment/.gitignore
Added  /trunk/madman/Rpacks/clusterExperiment/.travis.yml
Modified  /trunk/madman/Rpacks/clusterExperiment/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterExperiment/NAMESPACE
Modified  /trunk/madman/Rpacks/clusterExperiment/NEWS
Modified  /trunk/madman/Rpacks/clusterExperiment/R/AllClasses.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/clusterD.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/clusterMany.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/clusterSingle.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/combineMany.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/internalFunctions.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/makeDendrogram.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/mergeClusters.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/plotClusters.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/plotHeatmap.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/plottingHelpers.R
Added  /trunk/madman/Rpacks/clusterExperiment/R/rsec.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/seqCluster.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/subsampleClustering.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/transformFunction.R
Modified  /trunk/madman/Rpacks/clusterExperiment/R/workflowClusters.R
Added  /trunk/madman/Rpacks/clusterExperiment/README.md
Modified  /trunk/madman/Rpacks/clusterExperiment/man/ClusterExperiment-class.Rd
Added  /trunk/madman/Rpacks/clusterExperiment/man/RSEC.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/clusterD.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/clusterMany.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/clusterSingle.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/makeDendrogram.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/mergeClusters.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/plotHeatmap.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/plottingFunctions.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/seqCluster.Rd
Modified  /trunk/madman/Rpacks/clusterExperiment/man/transform.Rd
Added  /trunk/madman/Rpacks/clusterExperiment/tests/checkClusterMany
Added  /trunk/madman/Rpacks/clusterExperiment/tests/checkClusterMany/L5_sumExp.rda
Added  /trunk/madman/Rpacks/clusterExperiment/tests/checkClusterMany/clusterManyTest.R
Added  /trunk/madman/Rpacks/clusterExperiment/tests/checkClusterMany/fixedClusterManyResult.txt
Added  /trunk/madman/Rpacks/clusterExperiment/tests/checkClusterMany/makeData.R
Added  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_RSEC.R
Modified  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_clusterMany.R
Modified  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_clusterSingle.R
Modified  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_constructor.R
Modified  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_dendrogram.R
Added  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_internalFunctions.R
Modified  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_mergeClusters.R
Modified  /trunk/madman/Rpacks/clusterExperiment/tests/testthat/test_plotting.R
Modified  /trunk/madman/Rpacks/clusterExperiment/vignettes/bibFile.bib
Modified  /trunk/madman/Rpacks/clusterExperiment/vignettes/clusterExperimentTutorial.Rmd
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/clusterExperimentTutorial.html
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/clusterCellsDocumentation.Rmd
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/clusterCellsDocumentation.html
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/clusterCellsTutorial_old.Rmd
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/clusterCellsTutorial_old.html
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/figure
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/figure/flowBasicClustering-1.png
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/figure/flowspreadSeq-1.png
Added  /trunk/madman/Rpacks/clusterExperiment/vignettes/oldVignette/figure/subsampling-1.png
Release 0.99.3
Revision: 119750
Author: y.liu2
Date: 2016-07-29T20:35:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/XBSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/XBSeq/NAMESPACE
Modified  /trunk/madman/Rpacks/XBSeq/NEWS
Modified  /trunk/madman/Rpacks/XBSeq/R/core_functions.R
Modified  /trunk/madman/Rpacks/XBSeq/R/methods.R
Modified  /trunk/madman/Rpacks/XBSeq/man/XBSeq.Rd
Modified  /trunk/madman/Rpacks/XBSeq/man/XBSeqTest.Rd
Added  /trunk/madman/Rpacks/XBSeq/man/apaUsage.Rd
Modified  /trunk/madman/Rpacks/XBSeq/vignettes/XBSeq.Rmd
merge from master

From: Yuanhang Liu <yuanhangliu.ok@gmail.com>
Revision: 119747
Author: v.obenchain
Date: 2016-07-29T20:25:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblTwoBit.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/man/updateResources.Rd
update man page; wrap BiocVersion in package_version()
Revision: 119746
Author: h.corradabravo
Date: 2016-07-29T20:21:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
version bump

From: Hector Corrada Bravo <hcorrada@gmail.com>
Revision: 119745
Author: h.corradabravo
Date: 2016-07-29T20:21:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizApp-class.R
fix bug in 'getCurrentLocation' request

From: Hector Corrada Bravo <hcorrada@gmail.com>
Revision: 119744
Author: h.corradabravo
Date: 2016-07-29T20:21:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
version bump

From: Hector Corrada Bravo <hcorrada@gmail.com>
Revision: 119742
Author: h.corradabravo
Date: 2016-07-29T20:21:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizApp-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/startEpiviz.R
Modified  /trunk/madman/Rpacks/epivizr/man/startEpiviz.Rd
add 'ws_host' parameter to 'startEpiviz'

From: Hector Corrada Bravo <hcorrada@gmail.com>
Revision: 119741
Author: h.corradabravo
Date: 2016-07-29T20:20:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Version bump

From: Hector Corrada Bravo <hcorrada@gmail.com>
Revision: 119740
Author: h.corradabravo
Date: 2016-07-29T20:20:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizApp-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/startEpiviz.R
Modified  /trunk/madman/Rpacks/epivizr/man/startEpiviz.Rd
parametrize browser function in 'startEpiviz'

From: Hector Corrada Bravo <hcorrada@gmail.com>
Revision: 119739
Author: m.riester
Date: 2016-07-29T19:14:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Added mean coverages to verbose output.
Revision: 119738
Author: c.warden
Date: 2016-07-29T19:05:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/COHCAP/CHANGES
Modified  /trunk/madman/Rpacks/COHCAP/DESCRIPTION
Modified  /trunk/madman/Rpacks/COHCAP/NAMESPACE
Modified  /trunk/madman/Rpacks/COHCAP/R/COHCAP.avg.by.site.R
Added  /trunk/madman/Rpacks/COHCAP/R/COHCAP.denovo.R
Added  /trunk/madman/Rpacks/COHCAP/man/COHCAP.denovo.Rd
added de-novo cluster function
Revision: 119737
Author: j.meskas
Date: 2016-07-29T18:44:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCL/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowCL/NAMESPACE
Modified  /trunk/madman/Rpacks/flowCL/R/flowCL.R
Modified  /trunk/madman/Rpacks/flowCL/R/rQueryFunctions.R
Modified  /trunk/madman/Rpacks/flowCL/R/supportingFunctions.R
Modified  /trunk/madman/Rpacks/flowCL/data/flowCL_archive.rda
Modified  /trunk/madman/Rpacks/flowCL/inst/NEWS
Modified  /trunk/madman/Rpacks/flowCL/inst/unitTests/test_connection.R
Modified  /trunk/madman/Rpacks/flowCL/man/flowCL-package.Rd
Modified  /trunk/madman/Rpacks/flowCL/man/flowCL.Rd
Modified  /trunk/madman/Rpacks/flowCL/tests/flowCL_unit_tests.R
Modified  /trunk/madman/Rpacks/flowCL/vignettes/flowCL.Rnw
Fixed one bug involving has_pmp: <http://purl.obolibrary.org/obo/RO_0002104> that occured with the updated ontology. Fixed bug where tag wasn't showing for markers in the (C) category of $Markers. Updated data file and vignette. Fixed bug where a direct query to the markers is no longer needed because of the change in the ontology. Changed CompInfo to Verbose to be more consistent with other packages.
Revision: 119736
Author: jspidlen
Date: 2016-07-29T18:41:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/R/fit_functions.R
Modified  /trunk/madman/Rpacks/flowQB/man/fit_beads.Rd
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
logicle width default changed from 0.5 to 1
Revision: 119735
Author: m.riester
Date: 2016-07-29T17:24:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Fixed warning in 2D grid search when no local optimum in purity range.
Revision: 119734
Author: l.pantano
Date: 2016-07-29T17:13:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
bump minor version

From: Lorena Pantano <lorena.pantano@gmail.com>
Revision: 119732
Author: v.obenchain
Date: 2016-07-29T16:46:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblFasta.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblTwoBit.R
code tidy in makeEnsemblTwoBit.R
Revision: 119731
Author: t.thurnherr
Date: 2016-07-29T15:52:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/rDGIdb/DESCRIPTION
Added  /trunk/madman/Rpacks/rDGIdb/README.md
Modified  /trunk/madman/Rpacks/rDGIdb/inst/CITATION
Modified  /trunk/madman/Rpacks/rDGIdb/vignettes/vignette.Rnw
Added missing author and missing file from last commit
Revision: 119729
Author: mtmorgan
Date: 2016-07-29T13:16:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSEABase/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSEABase/R/methods-GeneSetCollection.R
performance: GO GeneSetCollection construction

- using template approach to populate
Revision: 119728
Author: p.blattmann
Date: 2016-07-29T11:52:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/DESCRIPTION
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/man/SWATH2stats-package.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/tests/testthat/test_filtering.R
v1.3.7: Bug fix in test_filtering

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 119727
Author: b.phipson
Date: 2016-07-29T04:17:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/DESCRIPTION
Modified  /trunk/madman/Rpacks/missMethyl/vignettes/missMethyl.Rnw
Modified vignette to try figure out where the bug is coming from: preprocessRaw or SWAN.
Revision: 119726
Author: m.riester
Date: 2016-07-29T03:39:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Fixed typos in vignette.
Revision: 119725
Author: g.yu
Date: 2016-07-29T03:05:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE
Modified  /trunk/madman/Rpacks/DOSE/.Rbuildignore
Modified  /trunk/madman/Rpacks/DOSE/.svnignore
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/NAMESPACE
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Added  /trunk/madman/Rpacks/DOSE/R/00-AllClasses.R
Added  /trunk/madman/Rpacks/DOSE/R/accessor.R
Modified  /trunk/madman/Rpacks/DOSE/R/cnetplot.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrichMap.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrichResult.R
Modified  /trunk/madman/Rpacks/DOSE/R/gseaResult.R
Modified  /trunk/madman/Rpacks/DOSE/README.md
Modified  /trunk/madman/Rpacks/DOSE/man/enrichResult-class.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/gseaResult-class.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/netplot.Rd
Deleted  /trunk/madman/Rpacks/DOSE/man/subset-methods.Rd
Deleted  /trunk/madman/Rpacks/DOSE/man/subset2-methods.Rd
Deleted  /trunk/madman/Rpacks/DOSE/man/subset3-methods.Rd
Modified  /trunk/madman/Rpacks/DOSE/vignettes/DOSE.Rmd
Added  /trunk/madman/Rpacks/DOSE/vignettes/GSEA.Rmd
Added  /trunk/madman/Rpacks/DOSE/vignettes/enrichmentAnalysis.Rmd
Added  /trunk/madman/Rpacks/DOSE/vignettes/figures
Added  /trunk/madman/Rpacks/DOSE/vignettes/figures/cnet_enrichDO.png
Added  /trunk/madman/Rpacks/DOSE/vignettes/figures/cnet_gseNCG.png
Added  /trunk/madman/Rpacks/DOSE/vignettes/figures/enrichMap_enrichDO.png
Added  /trunk/madman/Rpacks/DOSE/vignettes/figures/enrichMap_gseNCG.png
Added  /trunk/madman/Rpacks/DOSE/vignettes/figures/upsetplot_enrichDO.png
Added  /trunk/madman/Rpacks/DOSE/vignettes/semanticAnalysis.Rmd
update vignettes
Revision: 119724
Author: m.riester
Date: 2016-07-28T23:51:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Version bump.
Revision: 119723
Author: m.riester
Date: 2016-07-28T23:50:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Added FAQ section about manual curation.
Revision: 119721
Author: jspidlen
Date: 2016-07-28T22:24:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
Vignette fix
Revision: 119720
Author: m.riester
Date: 2016-07-28T22:09:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/filterVcf.R
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/man/filterVcfBasic.Rd
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Clarified scope of 'following steps' in vignette, added tests for VCF in single mode. Added warning when there was no SNP blacklist provided.
Revision: 119719
Author: v.obenchain
Date: 2016-07-28T21:43:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeUCSCChain.R
more tidy of unit tests
Revision: 119718
Author: v.obenchain
Date: 2016-07-28T21:37:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHubData/vignettes/ExperimentHubData.Rmd
update vigentte with zzz.R details
Revision: 119715
Author: k.oneill
Date: 2016-07-28T20:03:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/contiBAIT/.travis.yml
Modified  /trunk/madman/Rpacks/contiBAIT/DESCRIPTION
Modified  /trunk/madman/Rpacks/contiBAIT/NAMESPACE
Modified  /trunk/madman/Rpacks/contiBAIT/R/AllClasses.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/BAIT.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/contiBAIT.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/ideogramPlot.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/locateMisorients.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/makeChrTable.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/mergeFlankedLGs.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/plotContigOrder.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/preprocessStrandTable.R
Modified  /trunk/madman/Rpacks/contiBAIT/R/strandSeqFreqTable.R
Added  /trunk/madman/Rpacks/contiBAIT/data/exampleContigOrder.rda
Modified  /trunk/madman/Rpacks/contiBAIT/inst/NEWS
Modified  /trunk/madman/Rpacks/contiBAIT/inst/examples/plotContigOrder.R
Modified  /trunk/madman/Rpacks/contiBAIT/inst/examples/thoroughBed.R
Added  /trunk/madman/Rpacks/contiBAIT/man/exampleContigOrder.Rd
Modified  /trunk/madman/Rpacks/contiBAIT/man/ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method.Rd
Modified  /trunk/madman/Rpacks/contiBAIT/man/plotContigOrder.Rd
Modified  /trunk/madman/Rpacks/contiBAIT/vignettes/contiBAIT.tex
import version 1.1.3 manually from github
Revision: 119714
Author: k.horan
Date: 2016-07-28T17:28:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChemmineR/vignettes/ChemmineR.Rmd
fixed vignette bug
Revision: 119713
Author: l.shepherd
Date: 2016-07-28T15:45:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/inst/unitTests/test_VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
Fixed bug in subsetting RangedVcfStack
Revision: 119710
Author: z.xu
Date: 2016-07-28T13:40:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/ENmix/DESCRIPTION
Modified  /trunk/madman/Rpacks/ENmix/vignettes/ENmix.Rnw
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119709
Author: e.wright
Date: 2016-07-28T13:27:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/DECIPHER/R/IdClusters.R
Minor update.
Revision: 119708
Author: m.teng
Date: 2016-07-28T13:20:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/rnaseqcomp/DESCRIPTION
Modified  /trunk/madman/Rpacks/rnaseqcomp/R/AllClasses.R
Modified  /trunk/madman/Rpacks/rnaseqcomp/man/check_rnaseqcomp.Rd
minor bug fixed
Revision: 119705
Author: p.blattmann
Date: 2016-07-28T07:28:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/DESCRIPTION
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/R/filter_all_peptides.R
Modified  /trunk/madman/Rpacks/SWATH2stats/man/SWATH2stats-package.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/vignettes/SWATH2stats_vignette.Rnw
v1.3.6: improve message in filter_all_peptides and do note evaluate MSstats in vignette to prevent error

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 119704
Author: w.shi
Date: 2016-07-28T06:17:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/CHANGELOG
Modified  /trunk/madman/Rpacks/Rsubread/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsubread/R/align.R
Modified  /trunk/madman/Rpacks/Rsubread/R/subjunc.R
Modified  /trunk/madman/Rpacks/Rsubread/man/align.Rd
coerce file name parameters to be of character type
Revision: 119701
Author: t.silva
Date: 2016-07-28T01:48:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAPrepare.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAquery_clinical.R
fixing vignette
Revision: 119699
Author: t.silva
Date: 2016-07-28T01:08:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/tcgaBiolinks.Rmd
fixing vignette
Revision: 119698
Author: m.teng
Date: 2016-07-27T21:45:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/rnaseqcomp/DESCRIPTION
Modified  /trunk/madman/Rpacks/rnaseqcomp/inst/CITATION
minor bug fixed
Revision: 119697
Author: b.friedman
Date: 2016-07-27T19:21:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnalysisPageServer/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnalysisPageServer/NAMESPACE
Modified  /trunk/madman/Rpacks/AnalysisPageServer/R/param.set.R
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/add.event.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/add.event.handler.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/analysis.link.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/analysis.page.link.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/analysis.page.of.current.app.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/annotate.analysis.page.svg.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/annotate.data.frame.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/apache.httpd.conf.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/aps.dataset.divs.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/aps.one.dataset.div.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/aps.urlEncode.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/array.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/autosignal.on.bloated.memory.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/bind.memory.checker.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/bool.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/build.service.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/check.memory.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/check.same.svgs.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/check.signal.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/checkPackageInstalled.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/checkRookForkForVignettes.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/clear.event.handlers.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/client.ip.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/combobox.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/compound.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/config.js.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/copy.front.end.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/current.app.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/custom.body.attr.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/custom.body.html.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/custom.html.headers.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/data.frame.to.json.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/data.frame.to.list.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/default.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/default.param.set.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/default.service.paramset.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/default.stylesheets.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/dieIfWindows.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/dies.ok.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/embed.APS.dataset.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/encode.datanode.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/eval.within.time.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/event.names.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/execute.handler.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/file.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/filterWidget.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/get.APS.outdir.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/get.page.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/getTraceback.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/has.event.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/has.page.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/ignore.lots.of.stuff.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/is.registry.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/kill.process.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/known.param.sizes.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/lives.ok.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/make.standard.ids.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/messageSectionName.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.FastRWeb.analysis.page.run.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.analysis.page.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.datanode.array.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.datanode.html.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.datanode.plot.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.datanode.simple.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.datanode.table.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.event.registry.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.registry.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.response.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/new.rook.analysis.page.app.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/pages.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/param.set.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/paramSetToJSON.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/persistent.param.dependencies.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/persistent.params.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/platformIsWindows.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/protect.rapache.memory.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/rapache.app.from.registry.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/rapache.trig.app.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/register.page.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/remove.event.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/remove.old.files.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/requestEnv.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/reset.APS.outdir.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/rook.analysis.page.server.landing.page.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/search.replace.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/select.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/service.link.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/set.APS.outdir.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/setup.APS.knitr.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/simple.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/sine.handler.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/slider.param.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/startRookAnalysisPageServer.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/static.analysis.page.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/static.analysis.page.query.string.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/test.package.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/trig.registry.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/trigger.event.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/tryKeepConditions.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/tryKeepTraceback.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/uniquify.ids.in.svg.files.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/urlDecode.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/urlEncode.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.array.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.bool.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.combobox.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.compound.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.file.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.labeled.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.param.list.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.select.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/validate.text.param.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.conditions.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.error.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.error.condition.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.error.traceback.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.is.error.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.messages.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.messages.conditions.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.messages.tracebacks.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.n.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.n.messages.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.n.warnings.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.tracebacks.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.value.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.warnings.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.warnings.conditions.Rd
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/vwc.warnings.tracebacks.Rd
fix roxygen warning in paramSetToJSON
Revision: 119696
Author: g.gloor
Date: 2016-07-27T19:16:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/ALDEx2/DESCRIPTION
Modified  /trunk/madman/Rpacks/ALDEx2/NAMESPACE
Modified  /trunk/madman/Rpacks/ALDEx2/NEWS
Modified  /trunk/madman/Rpacks/ALDEx2/R/AllClasses.R
Modified  /trunk/madman/Rpacks/ALDEx2/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/ALDEx2/R/aldex.r
Modified  /trunk/madman/Rpacks/ALDEx2/R/clr_corr.R
Modified  /trunk/madman/Rpacks/ALDEx2/R/clr_effect.r
Modified  /trunk/madman/Rpacks/ALDEx2/R/clr_function.r
Modified  /trunk/madman/Rpacks/ALDEx2/R/clr_glm.r
Modified  /trunk/madman/Rpacks/ALDEx2/R/clr_ttest.r
Added  /trunk/madman/Rpacks/ALDEx2/R/iqlr_features.r
Modified  /trunk/madman/Rpacks/ALDEx2/data/selex.txt.gz
Modified  /trunk/madman/Rpacks/ALDEx2/inst/CITATION
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.clr-class.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.clr.function-methods.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.corr.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.effect.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.glm.Rd
Added  /trunk/madman/Rpacks/ALDEx2/man/aldex.set.mode.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/aldex.ttest.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/getFeatureNames-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/getFeatures-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/getMonteCarloInstances-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/getMonteCarloReplicate-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/getReads-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/getSampleIDs-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/numConditions-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/numFeatures-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/numMCInstances-method.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/man/selex.Rd
Modified  /trunk/madman/Rpacks/ALDEx2/vignettes/ALDEx2_vignette.Rnw
added ability to deal with asymmetric data

From: ggloor <ggloor@uwo.ca>
Revision: 119695
Author: m.ramos
Date: 2016-07-27T18:29:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Added  /trunk/madman/Rpacks/GenomicRanges/R/makeGRangesListFromDataFrame.R
Added  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_makeGRangesListFromDataFrame.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GRanges-class.Rd
Added  /trunk/madman/Rpacks/GenomicRanges/man/makeGRangesListFromDataFrame.Rd
Add makeGRangesListFromDataFrame function, tests, and docs.
Document seqinfo,*-method and register .DollarNames.GenomicRanges
Revision: 119693
Author: t.silva
Date: 2016-07-27T18:05:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAPrepare.R
fixing non ascii char
Revision: 119692
Author: t.silva
Date: 2016-07-27T17:55:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAPrepare.R
improving download
Revision: 119683
Author: khansen
Date: 2016-07-27T15:23:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified  /trunk/madman/Rpacks/minfi/R/preprocess.R
Modified  /trunk/madman/Rpacks/minfi/R/read.meth.R
Modified  /trunk/madman/Rpacks/minfi/inst/NEWS.Rd
merged version 1.19.12 from Github
Revision: 119682
Author: g.hoffman
Date: 2016-07-27T14:51:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/variancePartition/DESCRIPTION
Modified  /trunk/madman/Rpacks/variancePartition/NEWS
Modified  /trunk/madman/Rpacks/variancePartition/R/fitModels.R
Modified  /trunk/madman/Rpacks/variancePartition/R/misc.R
v1.3.7
Revision: 119679
Author: m.lawrence
Date: 2016-07-27T13:29:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VRanges-class.R
use [["FT"]] to avoid picking up FTZ field
Revision: 119678
Author: mtmorgan
Date: 2016-07-27T13:12:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/NEWS
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-RsamtoolsFile.R
Added  /trunk/madman/Rpacks/Rsamtools/inst/unitTests/test_RsamtoolsFile.R
bugfix: RsamtoolsFile argument lengths

- must be 1 for 'path', 0 or 1 for 'index'
Revision: 119677
Author: g.yu
Date: 2016-07-27T05:17:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/geom_strip.R
update geom_strip
Revision: 119674
Author: g.yu
Date: 2016-07-27T04:25:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/R/geom_strip.R
Modified  /trunk/madman/Rpacks/ggtree/R/tree-utilities.R
Added  /trunk/madman/Rpacks/ggtree/man/nodeid.Rd
Modified  /trunk/madman/Rpacks/ggtree/vignettes/ggtreeUtilities.Rmd
update geom_strip and add nodeid function
Revision: 119672
Author: l.goldstein
Date: 2016-07-27T01:48:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/annotation.R
Modified  /trunk/madman/Rpacks/SGSeq/R/convert.R
Modified  /trunk/madman/Rpacks/SGSeq/R/graphs.R
Changes in SGSeq 1.7.7 - Bug fixes

- SGVariants geneNames now based on the union of included SGFeatures geneNames
- ensure variantNames are unique
- avoid warnings in findSGVariants()
- preserve txName and geneName in convertToSGFeatures with coerce = TRUE
Revision: 119668
Author: mtmorgan
Date: 2016-07-26T22:10:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/DESCRIPTION
Summary: version bump
Revision: 119667
Author: mtmorgan
Date: 2016-07-26T22:09:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/man/Assays-class.Rd
Modified  /trunk/madman/Rpacks/SummarizedExperiment/man/SummarizedExperiment-class.Rd
Summary: document [,*,ANY,ANY,ANY

- for SummarizedExperiment, Assay
Revision: 119666
Author: mtmorgan
Date: 2016-07-26T22:08:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/NAMESPACE
Summary: register .DollarName.SummarizedExperiment
Revision: 119665
Author: s.munro
Date: 2016-07-26T20:56:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/erccdashboard/DESCRIPTION
Modified  /trunk/madman/Rpacks/erccdashboard/NEWS
Modified  /trunk/madman/Rpacks/erccdashboard/R/dynRangePlot.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/estLODR.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/est_r_m.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/maSignal.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/normalizeDat.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/runDashboard.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/saveERCCPlots.R
Modified  /trunk/madman/Rpacks/erccdashboard/R/testDEArray.R
Modified  /trunk/madman/Rpacks/erccdashboard/man/annotLODR.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/dynRangePlot.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/erccROC.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/estLODR.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/est_r_m.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/geneExprTest.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/initDat.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/maSignal.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/runDashboard.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/man/saveERCCPlots.Rd
Modified  /trunk/madman/Rpacks/erccdashboard/vignettes/erccdashboard.Rnw
fixed DESCRIPTION conflict

Merge branch 'master' into devel

* master:
  trying to eliminate Rplots.pdf artifact from runDashboard on commandline
  trying to eliminate Rplots.pdf artifact from runDashboard on commandline
  fix to show.legend and repNormFactors for microarray data.

# Conflicts:
#	DESCRIPTION

From: Sarah Munro <sarah.munro@nist.gov>
Revision: 119664
Author: z.xu
Date: 2016-07-26T20:17:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/ENmix/DESCRIPTION
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119663
Author: z.xu
Date: 2016-07-26T20:14:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/ENmix/NAMESPACE
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119662
Author: z.xu
Date: 2016-07-26T20:12:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/ENmix/NAMESPACE
Modified  /trunk/madman/Rpacks/ENmix/R/ComBat.mc.R
Modified  /trunk/madman/Rpacks/ENmix/R/QCfilter.R
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119661
Author: z.xu
Date: 2016-07-26T20:12:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/ENmix/DESCRIPTION
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119660
Author: z.xu
Date: 2016-07-26T20:12:10+00:00
Paths:
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_afterQC.jpg
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_beforeQC.jpg
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_CpG.jpg
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_sample.jpg
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119659
Author: z.xu
Date: 2016-07-26T20:12:02+00:00
Paths:
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_afterQC.jpg
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_beforeQC.jpg
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_CpG.jpg
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_sample.jpg
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119658
Author: z.xu
Date: 2016-07-26T20:11:53+00:00
Paths:
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_afterQC.jpg
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_beforeQC.jpg
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_CpG.jpg
Deleted  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_sample.jpg
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
Revision: 119657
Author: z.xu
Date: 2016-07-26T20:11:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/ENmix/DESCRIPTION
Modified  /trunk/madman/Rpacks/ENmix/NAMESPACE
Modified  /trunk/madman/Rpacks/ENmix/R/ComBat.mc.R
Modified  /trunk/madman/Rpacks/ENmix/R/QCfilter.R
Modified  /trunk/madman/Rpacks/ENmix/R/QCinfo.R
Modified  /trunk/madman/Rpacks/ENmix/R/bmiq.mc.R
Modified  /trunk/madman/Rpacks/ENmix/R/ctrlsva.R
Modified  /trunk/madman/Rpacks/ENmix/R/multifreqpoly.R
Modified  /trunk/madman/Rpacks/ENmix/R/nmode.mc.R
Modified  /trunk/madman/Rpacks/ENmix/R/norm.quantile.R
Modified  /trunk/madman/Rpacks/ENmix/R/normalize.quantile.450k.R
Modified  /trunk/madman/Rpacks/ENmix/R/oxBS.MLE.R
Modified  /trunk/madman/Rpacks/ENmix/R/pcrplot.R
Modified  /trunk/madman/Rpacks/ENmix/R/plotCtrl.R
Modified  /trunk/madman/Rpacks/ENmix/R/preprocessENmix.R
Modified  /trunk/madman/Rpacks/ENmix/R/rcp.R
Modified  /trunk/madman/Rpacks/ENmix/R/relic.R
Modified  /trunk/madman/Rpacks/ENmix/R/rm.outlier.R
Modified  /trunk/madman/Rpacks/ENmix/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/ENmix/inst/doc/ENmix.R
Modified  /trunk/madman/Rpacks/ENmix/inst/doc/ENmix.pdf
Added  /trunk/madman/Rpacks/ENmix/inst/testData/.testData.ls.swp
Modified  /trunk/madman/Rpacks/ENmix/inst/testData/testData.R
Modified  /trunk/madman/Rpacks/ENmix/inst/testData/testData.out
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_afterQC.jpg
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/freqpolygon_beta_beforeQC.jpg
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_CpG.jpg
Added  /trunk/madman/Rpacks/ENmix/inst/unitTests/qc_sample.jpg
Modified  /trunk/madman/Rpacks/ENmix/inst/unitTests/testDigests.rda
Modified  /trunk/madman/Rpacks/ENmix/inst/unitTests/test_enmix.R
Modified  /trunk/madman/Rpacks/ENmix/man/QCfilter.Rd
Modified  /trunk/madman/Rpacks/ENmix/man/QCinfo.Rd
Modified  /trunk/madman/Rpacks/ENmix/man/ctrlsva.Rd
Modified  /trunk/madman/Rpacks/ENmix/man/rm.outlier.Rd
Modified  /trunk/madman/Rpacks/ENmix/vignettes/ENmix.Rnw
commit made by Xu

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>

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