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

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


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

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

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

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

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

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

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

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

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

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

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

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

no longer actively developed

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

From: Robert Scharpf <rscharpf@jhu.edu>
Revision: 121519
Author: t.silva
Date: 2016-09-28T23:43:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/man/GDCdownload.Rd
verifying input in survival
Revision: 121518
Author: t.silva
Date: 2016-09-28T23:43:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGADownload.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/methylation.R
verifying input in survival
Revision: 121517
Author: m.lawrence
Date: 2016-09-28T21:41:13+00:00
Paths:
Added  /trunk/madman/Rpacks/rsbml/INSTALL
add INSTALL file with Windows build instructions
Revision: 121516
Author: t.silva
Date: 2016-09-28T21:37:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/DESCRIPTION
version bump
Revision: 121514
Author: t.silva
Date: 2016-09-28T21:25:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGADownload.R
fixingif http cannot be read
Revision: 121513
Author: l.zhu
Date: 2016-09-28T20:54:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/GUIDEseq/R/GUIDEseqAnalysis.R
fixed a bug when one of the two libraries have no peaks
Revision: 121512
Author: m.lawrence
Date: 2016-09-28T20:39:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/AtomicList-impl.R
as.matrix.AtomicList() decodes Rle data
Revision: 121511
Author: m.lawrence
Date: 2016-09-28T20:38:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/AtomicList-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/CompressedList-comparison.R
fixes to unique/duplicated List methods
Revision: 121510
Author: m.lawrence
Date: 2016-09-28T20:38:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/ListGrouping-class.R
fixes to ManyToOneGrouping=>factor coercion
Revision: 121509
Author: m.lawrence
Date: 2016-09-28T20:37:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
findOverlapPairs() allows 'subject' to be missing for self pairing
Revision: 121508
Author: m.lawrence
Date: 2016-09-28T20:36:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/extractList.R
when grouping, ensure lone element in list is coerced to factor
Revision: 121507
Author: v.obenchain
Date: 2016-09-28T19:50:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationForge/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationForge/inst/extdata/GentlemanLab/ANNDBPKG-INDEX.TXT
bump OrgDb versions for Bioconductor 3.4 release
Revision: 121502
Author: s.neumann
Date: 2016-09-28T19:33:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/.travis.yml
Don't treat warnings_are_errors
Revision: 121501
Author: t.silva
Date: 2016-09-28T19:09:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/DESCRIPTION
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAvisualize.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/man/TCGAvisualize_profilePlot.Rd
fixing profile plot
Revision: 121500
Author: l.waldron
Date: 2016-09-28T18:49:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/doppelgangR/DESCRIPTION
Modified  /trunk/madman/Rpacks/doppelgangR/tests/maintest.R
Updated unit tests for change in ExpressionSet behavior.
Revision: 121499
Author: rscharpf
Date: 2016-09-28T18:40:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/oligoClasses/DESCRIPTION
Modified  /trunk/madman/Rpacks/oligoClasses/man/makeFeatureGRanges.Rd
Bumped version

From: Robert Scharpf <rscharpf@jhu.edu>
Revision: 121498
Author: rscharpf
Date: 2016-09-28T18:40:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/oligoClasses/man/makeFeatureGRanges.Rd
Fix example makeFeatureGRanges example

From: Robert Scharpf <rscharpf@jhu.edu>
Revision: 121497
Author: k.rue-albrecht
Date: 2016-09-28T17:27:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOexpress/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOexpress/R/analysis.R
Modified  /trunk/madman/Rpacks/GOexpress/man/GO_analyse.Rd
Allow choice of host and biomart database to retrieve annotations from.
Revision: 121494
Author: p.angerer
Date: 2016-09-28T15:56:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/DESCRIPTION
v1.99.15
Revision: 121490
Author: r.stark
Date: 2016-09-28T15:34:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/DiffBind/DESCRIPTION
Modified  /trunk/madman/Rpacks/DiffBind/R/DBA.R
Modified  /trunk/madman/Rpacks/DiffBind/R/core.R
Modified  /trunk/madman/Rpacks/DiffBind/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/DiffBind/man/dba.plotPCA.Rd
add fromComp option to dba.plotPCA
Revision: 121488
Author: a.pickering
Date: 2016-09-28T14:56:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/crossmeta/DESCRIPTION
Modified  /trunk/madman/Rpacks/crossmeta/R/selection_utils.R
Modified  /trunk/madman/Rpacks/crossmeta/README.md
Deleted  /trunk/madman/Rpacks/crossmeta/vignettes/Vignette.R
Deleted  /trunk/madman/Rpacks/crossmeta/vignettes/Vignette.Rmd
Deleted  /trunk/madman/Rpacks/crossmeta/vignettes/Vignette.html
Added  /trunk/madman/Rpacks/crossmeta/vignettes/crossmeta-vignette.Rmd
Merge branch 'master' into remotes/hedgehog

Conflicts:
	DESCRIPTION
	vignettes/Vignette.R
	vignettes/Vignette.html
Revision: 121487
Author: s.neumann
Date: 2016-09-28T14:41:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/DESCRIPTION
Modified  /trunk/madman/Rpacks/CAMERA/inst/NEWS
Bump version and add NEWS
Revision: 121486
Author: s.neumann
Date: 2016-09-28T14:41:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/vignettes/IsotopeDetectionVignette.Rnw
Modified  /trunk/madman/Rpacks/CAMERA/vignettes/compoundQuantilesVignette.Rnw
Fix vignettes
Revision: 121485
Author: s.neumann
Date: 2016-09-28T14:41:39+00:00
Paths:
Added  /trunk/madman/Rpacks/CAMERA/vignettes/IsotopeDetectionVignette.Rnw
Modified  /trunk/madman/Rpacks/CAMERA/vignettes/compoundQuantilesVignette.Rnw
added vignette for the isotope detection pipeline;
updated vignette for compoundQuantiles
Revision: 121484
Author: s.neumann
Date: 2016-09-28T14:41:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/R/fct_findIsotopesWithValidation.R
Modified  /trunk/madman/Rpacks/CAMERA/man/findIsotopesWithValidation-methods.Rd
added database parameter to function findIsotopesWithValidation
Revision: 121483
Author: s.neumann
Date: 2016-09-28T14:41:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/R/fct_findIsotopesWithValidation.R
bug fix for R 3.3
Revision: 121482
Author: t.sandmann
Date: 2016-09-28T14:40:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/gCMAP/DESCRIPTION
Modified  /trunk/madman/Rpacks/gCMAP/R/camera_score-methods.R
Modified  /trunk/madman/Rpacks/gCMAP/inst/NEWS.Rd
added camera's new inter.gene.cor argument to the call in camera_score-methods.R
Revision: 121481
Author: t.hardcastle
Date: 2016-09-28T13:21:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/baySeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/baySeq/R/countData-accessors.R
Modified  /trunk/madman/Rpacks/baySeq/R/topCounts.R
2.7.7 tweak to topCounts to remove warning if selecting by multiple attributes; tweak to show countData method to only try and show data if present.
Revision: 121480
Author: c.pacini
Date: 2016-09-28T12:30:27+00:00
Paths:
Added  /trunk/madman/Rpacks/covEB/man/EBsingle.Rd
add EBsingle.Rd documentation
Revision: 121479
Author: d.ramazzotti
Date: 2016-09-28T12:21:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/OncoScore/DESCRIPTION
Modified  /trunk/madman/Rpacks/OncoScore/vignettes/vignette.Rnw
update to 1.1.2
Revision: 121477
Author: a.wachter
Date: 2016-09-28T11:48:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/pwOmics/DESCRIPTION
Modified  /trunk/madman/Rpacks/pwOmics/R/pwOmics_helper_functions.R
Modified  /trunk/madman/Rpacks/pwOmics/R/pwOmics_read_data.R
Modified  /trunk/madman/Rpacks/pwOmics/man/OmicsExampleData.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/PWidentallprots.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/PWidentallprotssub.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/PWidenttps.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/SteinerTree_cons.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/TFidentallgenes.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/TFidenttps.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/addFeedbackLoops.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/clusterTimeProfiles.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/consDynamicNet.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/createBiopaxnew.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/createIntIDs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/enrichPWs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/enrichTFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/findxneighborsoverlap.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/findxnextneighbors.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/genGenelists.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/genGenelistssub.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/genIntIDs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/genfullConsensusGraph.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getAlias_Ensemble.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getAliasfromSTRINGIDs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getBiopaxModel.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getConsensusSTRINGIDs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getDS_PWs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getDS_TFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getDS_TGs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getFCsplines.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getGenesIntersection.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getOmicsDataset.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getOmicsTimepoints.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getOmicsallGeneIDs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getOmicsallProteinIDs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getProteinIntersection.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getSTRING_graph.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getTFIntersection.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getUS_PWs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getUS_TFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getUS_regulators.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/getbipartitegraphInfo.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/gettpIntersection.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identPWsofTFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identRegulators.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identTFTGsinPWs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identTFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identifyPWTFTGs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identifyPWs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identifyRsofTFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/identifyTFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/loadGenelists.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/loadPWs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/plotConsDynNet.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/plotConsensusGraph.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/plotConsensusProfiles.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/plotTimeProfileClusters.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/predictFCvals.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/preparePWinfo.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/print.OmicsData.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/readOmics.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/readPWdata.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/readTFdata.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/readTFtargets.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/selectPWsofTFs.Rd
Modified  /trunk/madman/Rpacks/pwOmics/man/staticConsensusNet.Rd
Modified  /trunk/madman/Rpacks/pwOmics/vignettes/pwOmics.Rnw
changed preamble in Rnw, use pazar for example, set Biomart host
Revision: 121476
Author: c.ruiz-arenas
Date: 2016-09-28T10:21:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/MultiDataSet/DESCRIPTION
Modified  /trunk/madman/Rpacks/MultiDataSet/vignettes/MultiDataSet.Rmd
Update vignette
Bump version

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