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Revision: 102865
Author: c.mchugh
Date: 2015-04-21T01:28:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAnD/DESCRIPTION
Modified  /trunk/madman/Rpacks/CAnD/R/getDiffMatrices.R
Modified  /trunk/madman/Rpacks/CAnD/R/nonParam_CAnD.R
fixed bug in getDiffMatricescd ..! also, called binom.test in nonParam_CAnD.R function, just discovered it
Revision: 102860
Author: hpages
Date: 2015-04-20T21:56:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/coverage-methods.R
add comment
Revision: 102859
Author: hpages
Date: 2015-04-20T21:53:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/coverage-methods.R
"coverage" methods now also accept 'shift' supplied as an Rle
Revision: 102858
Author: m.jiang
Date: 2015-04-20T21:48:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingHierarchy-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSet-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/R/zzz.R
Modified  /trunk/madman/Rpacks/flowWorkspace/man/getSingleCellExpression.Rd
Modified  /trunk/madman/Rpacks/flowWorkspace/man/plotGate-methods.Rd
Modified  /trunk/madman/Rpacks/flowWorkspace/src/R_GatingHierarchy.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/vignettes/flowWorkspace.Rnw
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8eba4034f36a2ac879a33508fa8ecb7cc3a1b471

    update vignette


Commit id: 1e4074d61ba3659de8415025f716891b6a77880a

    merge from master


Commit id: de262246ed560221c043e4179cc0444f5fce549d

    add more global parameters for plotGate


Commit id: 24b28fd3afa5c98dfd8fb9e9fa701d2c28e0c91f

    add 'other.markers' argument to getSingleCellExpression call to optional return more markers when threshold=F


Commit id: 4fce65f96883bfba01ced2f3758bb1707c68ae47

    add histogram support to plotGate

Revision: 102857
Author: m.jiang
Date: 2015-04-20T21:45:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowCore/R/coerce.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b8638fd1eb0bce8e31f1405fa00ed1e44543247b

    sort the sample names before assigning it back to flowSet. close #35


Commit id: 07e9b2f3ec8b2b33b9aeb4f5ceec83598d363d2e

    Merge pull request #36 from RGLab/gfinak-patch-1

    Add Mike's name to authors as he's made substantial updates to the package

Commit id: aa893e6b428971695599a17c19c955b3fe370e3e

    Add Mike's name to authors as he's made substantial updates to the package.

Revision: 102856
Author: hpages
Date: 2015-04-20T21:38:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/coverage-methods.R
"coverage" methods now accept 'shift' and 'weight' supplied as an Rle
Revision: 102855
Author: hpages
Date: 2015-04-20T21:26:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/coverage-methods.R
"coverage" methods now accept 'weight' supplied as an Rle
Revision: 102854
Author: k.mezhoud
Date: 2015-04-20T20:55:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/canceR/DESCRIPTION
Modified  /trunk/madman/Rpacks/canceR/NAMESPACE
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e9a2d7d85dde55acac7d8cb976bed7bd15fa4e2f

    1.1.0

Revision: 102853
Author: m.jiang
Date: 2015-04-20T20:33:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowViz/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowViz/NAMESPACE
Modified  /trunk/madman/Rpacks/flowViz/R/histogram.R
Modified  /trunk/madman/Rpacks/flowViz/man/densityplot.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7554b129d0de7847a5e3f06175617b24ba9a9b61

    doc histogram plot

Revision: 102852
Author: m.jiang
Date: 2015-04-20T20:32:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/ncdfFlow/DESCRIPTION
Modified  /trunk/madman/Rpacks/ncdfFlow/NAMESPACE
Modified  /trunk/madman/Rpacks/ncdfFlow/R/ncdfFlowSet-plot-methods.R
Modified  /trunk/madman/Rpacks/ncdfFlow/README
Modified  /trunk/madman/Rpacks/ncdfFlow/man/Indices.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/as.flowSet.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/clone.ncdfFlowSet.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/extractFlowFrame.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/flowSet-accessor.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/getFileName.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/lapply-methods.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncdfFlow.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncdfFlowList-class.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncdfFlowSet-Subset.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncdfFlowSet-class.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncdfFlowSet-constructor.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncdfFlowSet-split.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/ncfsApply-ncdfFlowSet-method.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/plot.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/rbind2-method.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/read.ncdfFlowSet.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/replacement-method-for-ncdfFlowSet.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/save_ncfs.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/subset-functions.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/subset-methods.Rd
Modified  /trunk/madman/Rpacks/ncdfFlow/man/unlink-ncdfFlowSet-method.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b9021ead78ddb0cd25bac062ed17fe78a03505cb

    bump version


Commit id: 4bbb2d714ddb047395cdcf83332cac55a3117e2e

    add flowViz::: to unexposed function call


Commit id: 5bc06eb378a1ebe52ecbb8f8b7ae6f6315df7b1b

    add histogram plot to ncdfFlow

Revision: 102851
Author: m.jiang
Date: 2015-04-20T20:22:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowViz/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowViz/NAMESPACE
Modified  /trunk/madman/Rpacks/flowViz/R/densityplot.R
Added  /trunk/madman/Rpacks/flowViz/R/histogram.R
Modified  /trunk/madman/Rpacks/flowViz/R/xyplot.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 581bf539a4ae7490cf2c201cf89d674dbc8648a2

    bump version


Commit id: cdf809c31afd2dec251e89c2268b7e660f7fb270

    support overlay as ncdfFlowList or ncdfFlowSet


Commit id: 002968fe4dd77d39d52e0e9386e6ab8934f6c749

    export panel.histogram.flowset


Commit id: 9afac50552a775b3d8e3afb9bf7e6f4c8a4a3745

    add histogram plot to flowViz


Commit id: 95b62dc4288831347c8b4e45876f762a06031835

    add overlay support for densityplot

Revision: 102850
Author: i.ihnatova
Date: 2015-04-20T19:52:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/ToPASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/ToPASeq/NAMESPACE
Added  /trunk/madman/Rpacks/ToPASeq/R/conversion_pathway.R
Modified  /trunk/madman/Rpacks/ToPASeq/R/grafikastypmihran.R
Modified  /trunk/madman/Rpacks/ToPASeq/man/pathway-class.Rd
Modified  /trunk/madman/Rpacks/ToPASeq/vignettes/ToPASeq.Rnw
fixing conversion problem by adding new functions
Revision: 102848
Author: hpages
Date: 2015-04-20T19:33:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Modified  /trunk/madman/Rpacks/rtracklayer/R/gff.R
Modified  /trunk/madman/Rpacks/rtracklayer/man/export.Rd
make import() work on a remote GFF or GTF file
Revision: 102846
Author: d.tenenbaum
Date: 2015-04-20T18:32:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/R/zzz.R
set BIOC_VERSION to 3.2!!!
Revision: 102845
Author: hpages
Date: 2015-04-20T18:27:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/RangedData-methods.R
Remove "seqnames" method for RangesList objects (has been buggy since its
introduction more than 2 years ago, stopped working months ago, was never
documented, is clearly not needed).
Revision: 102844
Author: m.jiang
Date: 2015-04-20T18:15:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowCore/R/AllClasses.R
Modified  /trunk/madman/Rpacks/flowCore/R/coerce.R
Modified  /trunk/madman/Rpacks/flowCore/inst/tests/test-flowSet-IO.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3b49e86e928e22671be62d8ddf122982f6bbdb80

    bump version


Commit id: 2092b815edccb1b1c7546e756596864722a50c3c

    fix the bug in coerce method. close #35


Commit id: 0118a2d4ea6819b835990028fc816c711959cb26

    increase 'm' value by one to avoid the logicle error due to too small 'm' value. #34

Revision: 102843
Author: hpages
Date: 2015-04-20T18:14:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/findSpliceOverlaps-methods.R
use splitAsList instead of seqsplit
Revision: 102841
Author: mtmorgan
Date: 2015-04-20T17:53:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/NEWS
Modified  /trunk/madman/Rpacks/Rsamtools/src/Template.h
bug fix -- segfault on range iteration

- part way through mate_inprogress_segments, all inprogress segments
  would be mated, but the algorithm continued to mate no-longer-valid
  reads. Occurred when reading a single BAM position resolved multiple
  mates
Revision: 102840
Author: s.arora
Date: 2015-04-20T17:48:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/R/getPackageRange.R
 code update


- change 3.1 to 3.2 for getPackageRange()

Revision: 102839
Author: e.fertig
Date: 2015-04-20T17:34:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/CoGAPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/CoGAPS/src/GibbsSampler.cpp
Modified  /trunk/madman/Rpacks/CoGAPS/src/GibbsSampler.h
Modified  /trunk/madman/Rpacks/CoGAPS/src/GibbsSamplerMap.cpp
Modified  /trunk/madman/Rpacks/CoGAPS/src/cogapsmapR.cpp
fixed bug in mapping version
Revision: 102838
Author: hpages
Date: 2015-04-20T17:29:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/NAMESPACE
don't import seqsplit anymore
Revision: 102837
Author: sdurinck
Date: 2015-04-20T17:13:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/biomaRt/DESCRIPTION
Modified  /trunk/madman/Rpacks/biomaRt/R/biomaRt.R
Modified  /trunk/madman/Rpacks/biomaRt/man/listEnsembl.Rd
Modified  /trunk/madman/Rpacks/biomaRt/man/useEnsembl.Rd
Ensembl function updates, now enabling to specify mirror
Revision: 102836
Author: d.tenenbaum
Date: 2015-04-20T17:12:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/R/zzz.R
indicate that restarting R is necessary
Revision: 102835
Author: d.tenenbaum
Date: 2015-04-20T17:05:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/inst/scripts/biocLite.R
Modify the biocLite.R script to offer some help to users unable to update
BiocInstaller 1.16.z.
Revision: 102832
Author: k.horan
Date: 2015-04-20T15:52:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChemmineR/R/sim.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7666180e5bcdbba7aa865421c95d6f2a79a2a7ce

    version 2.21.1


Commit id: b78fa51f1e06a9f8ba6a1f2a73831556a66463af

    Merge branch 'evalue_scale_fix'


Commit id: 2c876aeec3099bd2d5fb28a4e40ca58d9eceb4f8

    make evalue computation in fpSim scaled to size of given db, not the training db

Revision: 102828
Author: k.rue-albrecht
Date: 2015-04-20T13:33:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOexpress/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOexpress/NEWS
Modified  /trunk/madman/Rpacks/GOexpress/R/post_analysis.R
Modified  /trunk/madman/Rpacks/GOexpress/man/GOexpress-package.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/heatmap_GO.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 029e2ea0be4a309e57fc916ec80671052b9363cc

    Version 1.3.1. Bug fix: heatmap margins could not be controlled by the user input. Restored now.

Revision: 102827
Author: l.gatto
Date: 2015-04-20T12:50:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/zzz.R
update startup message
Revision: 102826
Author: l.gatto
Date: 2015-04-20T12:50:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/zzz.R
update how vigs are added to win menu
Revision: 102825
Author: l.gatto
Date: 2015-04-20T12:50:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnbase-package.Rd
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-development.Rnw
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-io.Rnw
update vignettes and package man
Revision: 102824
Author: l.gatto
Date: 2015-04-20T12:50:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/man/averageMSnSet.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_average.R
update averageMSnSet Rd/test for MSnSetList usage
Revision: 102823
Author: l.gatto
Date: 2015-04-20T12:50:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-demo.Rnw
fix \code to \Rfunction
Revision: 102822
Author: l.gatto
Date: 2015-04-20T12:49:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-demo.Rnw
reflect averageMSnSet's new MSnSetList input in vignette
Revision: 102821
Author: l.gatto
Date: 2015-04-20T12:49:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/compfnames.R
cleaning trailing spaces
Revision: 102820
Author: l.gatto
Date: 2015-04-20T12:49:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-demo.Rnw
add MSnSetList, split/unsplit ref to demo vignette
Revision: 102819
Author: l.gatto
Date: 2015-04-20T12:49:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/averageMSnSet.R
averageMSnSet uses MSnSetLists instead of lists of MSnSets
Revision: 102818
Author: l.gatto
Date: 2015-04-20T12:49:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
export split method
Revision: 102817
Author: l.gatto
Date: 2015-04-20T12:49:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-MSnSet.R
fix type in code
Revision: 102816
Author: l.gatto
Date: 2015-04-20T12:49:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Deleted  /trunk/madman/Rpacks/MSnbase/TODO.org
document changes
Revision: 102815
Author: l.gatto
Date: 2015-04-20T12:49:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-MSnSetList.R
remove trailing new line
Revision: 102814
Author: l.gatto
Date: 2015-04-20T12:48:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MSnSet.R
commonFeatureNames unit test
Revision: 102813
Author: l.gatto
Date: 2015-04-20T12:48:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-MSnSetList.R
MSnSetList methods/accessors
Revision: 102812
Author: l.gatto
Date: 2015-04-20T12:48:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/DataClasses.R
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnSetList-class.Rd
new MSnSetList class
Revision: 102811
Author: l.gatto
Date: 2015-04-20T12:48:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/man/commonFeatureNames.Rd
new commonFeatureNames function
Revision: 102810
Author: l.gatto
Date: 2015-04-20T12:48:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/utils.R
Added  /trunk/madman/Rpacks/MSnbase/man/compareMSnSets.Rd
new compareMSnSets function
Revision: 102809
Author: l.gatto
Date: 2015-04-20T12:48:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnSetList-class.Rd
fix MSnSetList man
Revision: 102808
Author: l.gatto
Date: 2015-04-20T12:47:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
export MSnSetList class
Revision: 102807
Author: l.gatto
Date: 2015-04-20T12:47:48+00:00
Paths:
Added  /trunk/madman/Rpacks/MSnbase/man/MSnSetList-class.Rd
new MSnSetList class documentation
Revision: 102806
Author: l.gatto
Date: 2015-04-20T12:47:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/R/utils.R
lintr fixes
Revision: 102805
Author: l.gatto
Date: 2015-04-20T12:47:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/R/DataClasses.R
Added  /trunk/madman/Rpacks/MSnbase/R/methods-MSnSetList.R
new MSnSetList class

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