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Revision: 117872
Author: jspidlen
Date: 2016-05-25T23:19:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/inst/NEWS
Added  /trunk/madman/Rpacks/flowQB/inst/unitTests
Added  /trunk/madman/Rpacks/flowQB/inst/unitTests/test_find_peak.R
Added  /trunk/madman/Rpacks/flowQB/tests
Added  /trunk/madman/Rpacks/flowQB/tests/runTests.R
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
Adding tests and resolving various check and BiocCheck issues.
Revision: 117871
Author: jspidlen
Date: 2016-05-25T22:58:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Modified  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
Resolving various check and BiocCheck issues
Revision: 117870
Author: y.liao
Date: 2016-05-25T22:42:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/HelperFunctions.c
Modified  /trunk/madman/Rpacks/Rsubread/src/SNPCalling.c
Modified  /trunk/madman/Rpacks/Rsubread/src/core.c
Modified  /trunk/madman/Rpacks/Rsubread/src/input-files.c
Modified  /trunk/madman/Rpacks/Rsubread/src/input-files.h
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
(1) probing max file pointers in featureCounts ; (2) allJunctions overshot chromosome bug
Revision: 117869
Author: jspidlen
Date: 2016-05-25T22:37:37+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowQB/inst/doc
Cleaning up
Revision: 117868
Author: jspidlen
Date: 2016-05-25T22:19:17+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowQB/R/flowQBCOMPACTEDFUNCTIONS_R.R
Added  /trunk/madman/Rpacks/flowQB/R/flowQBCOMPACTEDFUNCTIONS_R.R.original
Refactoring.
Revision: 117867
Author: jspidlen
Date: 2016-05-25T22:18:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Refactoring.
Revision: 117866
Author: jspidlen
Date: 2016-05-25T22:14:21+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowQB/man/flowQB-package.Rd
Added  /trunk/madman/Rpacks/flowQB/man/flowQB-package.Rd.original
Refactoring.
Revision: 117864
Author: jspidlen
Date: 2016-05-25T21:45:22+00:00
Paths:
Added  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd
Deleted  /trunk/madman/Rpacks/flowQB/man/find_peak.Rd.original
Putting find_peak back
Revision: 117863
Author: jspidlen
Date: 2016-05-25T21:34:06+00:00
Paths:
Added  /trunk/madman/Rpacks/flowQB/R/helperFunctions.R
Starting refactoring.
Revision: 117862
Author: jspidlen
Date: 2016-05-25T21:33:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/NAMESPACE
Modified  /trunk/madman/Rpacks/flowQB/R/flowQBCOMPACTEDFUNCTIONS_R.R
Starting refactoring.
Revision: 117860
Author: a.lun
Date: 2016-05-25T20:38:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/diffHic/inst/NEWS.Rd
Bumped version number in NEWS.
Revision: 117857
Author: m.jiang
Date: 2016-05-25T19:55:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/NAMESPACE
Modified  /trunk/madman/Rpacks/openCyto/R/gtMethod-methods.R
import parameters from flowCore to avoid warnings when openCyto is imported by others.
Revision: 117856
Author: p.haverty
Date: 2016-05-25T18:47:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/NAMESPACE
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Modified  /trunk/madman/Rpacks/genoset/man/pos-methods.Rd
Version: 1.29.4. 'pos' generic is now imported from GenomicRanges
Revision: 117855
Author: p.haverty
Date: 2016-05-25T18:40:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Version: 1.29.3. subsetting uses rowRanges getter rather than direct access
Revision: 117854
Author: m.jiang
Date: 2016-05-25T18:35:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/openCyto/NAMESPACE
Added  /trunk/madman/Rpacks/openCyto/R/toggle.helperGates.R
Added  /trunk/madman/Rpacks/openCyto/man/toggle.helperGates.Rd
add toggle.helperGates
Revision: 117851
Author: d.tenenbaum
Date: 2016-05-25T18:10:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/bamsignals/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/deepSNV/DESCRIPTION
Modified  /trunk/madman/Rpacks/diffHic/DESCRIPTION
Bump version of packages that directly depend on Rhtslib, now that it is
linking against htslib statically.
Revision: 117850
Author: d.tenenbaum
Date: 2016-05-25T18:06:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rhtslib/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rhtslib/R/zzz.R
Link htslib statically
Revision: 117849
Author: l.shepherd
Date: 2016-05-25T17:10:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
Add Subsetting Functions and update readVcfStack

Revision: 117847
Author: p.blattmann
Date: 2016-05-25T15:43:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/R/convert4MSstats.R
v1.3.4b update message in convert4MSstats.R

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 117845
Author: m.scherer
Date: 2016-05-25T15:20:56+00:00
Paths:
Added  /trunk/madman/Rpacks/RnBeads/man/add.age.histogram.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.agecomparison.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.combination.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.error.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/add.quantile.plot.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/age.anti.transformation.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/age.transformation.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/agePredictor.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/agePredictor450.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/agePredictorRRBS.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/createPredictor.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/cv.array.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/cv.biseq.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/general.cv.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/imputeRRBS.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.execute.age.prediction.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.execute.training.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.section.ageprediction.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/rnb.step.ageprediction.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/run.cross.validation.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/simpleGlmnet.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/simpleGlmnetEvaluate.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/simpleGlmnetRRBS.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/trainPredictor.Rd
Added  /trunk/madman/Rpacks/RnBeads/man/writePredictorToCsv.Rd
More documentation on age prediction
Revision: 117844
Author: m.scherer
Date: 2016-05-25T15:14:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/DESCRIPTION
Modified  /trunk/madman/Rpacks/RnBeads/NAMESPACE
Modified  /trunk/madman/Rpacks/RnBeads/R/agePrediction.R
Running devtools for documentation of the new functions in the age prediction
Revision: 117843
Author: p.blattmann
Date: 2016-05-25T14:45:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/DESCRIPTION
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/R/convert4mapDIA.R
Modified  /trunk/madman/Rpacks/SWATH2stats/R/plot_correlation_between_samples.R
Modified  /trunk/madman/Rpacks/SWATH2stats/R/plot_variation.R
Modified  /trunk/madman/Rpacks/SWATH2stats/man/SWATH2stats-package.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/man/plot_correlation_between_samples.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/tests/testthat/test_convert.R
v1.3.4: convert4mapDIA: improve error message; plot_correlation_between_samples: add label option; plot_variation; DESCRIPTION

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 117839
Author: m.scherer
Date: 2016-05-25T13:20:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/main.R
Modified  /trunk/madman/Rpacks/RnBeads/inst/extdata/options.txt
Added options inference.age.prediction.cv and inference.age.column
Revision: 117838
Author: m.scherer
Date: 2016-05-25T13:19:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/vignettes/RnBeads.Rnw
Added age prediction section to package vignette
Revision: 117837
Author: m.scherer
Date: 2016-05-25T13:19:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/agePrediction.R
Added cross validation for training function
Revision: 117836
Author: l.shepherd
Date: 2016-05-25T13:00:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
Updated Constructor

  - no arguments have to be specified
  - auto generates seqinfo if not provided
  - auto generates colData if not provided
  - removed VcfHeader information from object
  - removed automatic subsetting of seqinfo object

Revision: 117835
Author: mtmorgan
Date: 2016-05-25T13:00:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/R/updateBiocInstaller.R
bugfix: unload rather than detach BiocInstaller on update

- also, catch failed attempts to unload for more informative error message
Revision: 117833
Author: f.marini
Date: 2016-05-25T09:41:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/pcaExplorer/R/pcaExplorer.R
mini fix for color assignments in genespca

From: Federico Marini <marinif@uni-mainz.de>
Revision: 117832
Author: k.bemis
Date: 2016-05-25T08:23:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/Cardinal/NEWS
Modified  /trunk/madman/Rpacks/Cardinal/R/methods-SImageData.R
v1.4.1 fixed SImageData subset bug
Revision: 117830
Author: a.oles
Date: 2016-05-25T07:58:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
version 4.15.3
- `readImage`: use `vapply` instead of `abind` to reduce memory footprint

From: aoles <andrzej.oles@gmail.com>
Revision: 117829
Author: j.rainer
Date: 2016-05-25T07:16:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensembldb/R/Methods.R
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Modified  /trunk/madman/Rpacks/ensembldb/inst/unitTests/test_Functionality.R
Fix another bug in exonsBy.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117828
Author: j.rainer
Date: 2016-05-25T06:38:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Merge finished.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117827
Author: j.rainer
Date: 2016-05-25T06:38:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/R/EnsDbFromGTF.R
Modified  /trunk/madman/Rpacks/ensembldb/R/Methods.R
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Bug fixes

o Column tx_id was always removed from exonsBy result even if in the
  columns argument.
o exon_idx was of type character if database generated from a GTF file.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117826
Author: j.rainer
Date: 2016-05-25T06:38:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/inst/NEWS
Update NEWS and DESCRIPTION.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 117824
Author: s.manimaran
Date: 2016-05-25T04:53:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/BatchQC/R/simulate_data.R
Modified  /trunk/madman/Rpacks/BatchQC/inst/example/batchqc_pipeline.R
Modified  /trunk/madman/Rpacks/BatchQC/tests/testthat/test_batchQC.R
Modified  /trunk/madman/Rpacks/BatchQC/vignettes/BatchQCIntro.Rmd
Modified  /trunk/madman/Rpacks/BatchQC/vignettes/BatchQC_examples.Rmd
Modified  /trunk/madman/Rpacks/BatchQC/vignettes/BatchQC_usage_advanced.Rmd
Changing the parameter for the example simulated dataset to lower the batch and condition variation for SVA to work well
Revision: 117819
Author: m.riester
Date: 2016-05-24T23:04:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Added message when intervals and SNVs not overlap.
Revision: 117818
Author: hpages
Date: 2016-05-24T22:37:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Deleted  /trunk/madman/Rpacks/IRanges/R/subsetting-internals.R
Added  /trunk/madman/Rpacks/IRanges/R/subsetting-utils.R
NSBS() generic (defined in S4Vectors) got new allow.NAs argument
Revision: 117817
Author: hpages
Date: 2016-05-24T22:34:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/R/DataFrame-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/Rle-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/subsetting-utils.R
normalizeSingleBracketSubscript() gets new 'allow.NAs' argument. This is used
in the "extractROWS" methods for atomic vectors and DataFrame objects to enable
support of NAs in the subscript.
Revision: 117815
Author: m.alhamdoosh
Date: 2016-05-24T22:17:39+00:00
Paths:
Added  /trunk/madman/Rpacks/EGSEA/R/EGSEAclass.R
Added  /trunk/madman/Rpacks/EGSEA/R/gsafry.R
added missing files
Revision: 117812
Author: l.shepherd
Date: 2016-05-24T18:41:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/R/VcfStack-class.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/VcfStack-class.Rd
added functionality

  - added dimnames()
  - more stringent validity
  - more readable show()

Revision: 117810
Author: m.riester
Date: 2016-05-24T17:46:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/findBestNormal.R
Modified  /trunk/madman/Rpacks/PureCN/man/findBestNormal.Rd
Added sex argument to findBestNormal. Add always three diploid solutions with purity < 1/3, > 1/3 and < 2/3 and >2/3 to list of candidate solutions. This makes sure that if the correct solution is diploid, we at least always try to search somewhere close.
Revision: 117809
Author: g.finak
Date: 2016-05-24T17:26:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/COMPASS/R/SimpleCOMPASS.R
Set a default random seed in simpleCOMPASS
Revision: 117806
Author: b.mifsud
Date: 2016-05-24T10:54:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOTHiC/DESCRIPTION
updated binomial test
Revision: 117805
Author: b.mifsud
Date: 2016-05-24T10:53:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOTHiC/R/GOTHiC.R
updated binomial test
Revision: 117803
Author: c.panse
Date: 2016-05-24T08:29:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/DESCRIPTION
Modified  /trunk/madman/Rpacks/specL/R/genSwathIonLib.R
Modified  /trunk/madman/Rpacks/specL/man/genSwathIonLib.Rd
add NORMALIZATION
Revision: 117798
Author: z.kurt
Date: 2016-05-24T04:25:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/Mergeomics/DESCRIPTION
Modified  /trunk/madman/Rpacks/Mergeomics/man/Mergeomics-package.Rd
Modified  /trunk/madman/Rpacks/Mergeomics/man/kda.analyze.Rd
Some examples are updated since the package could not be built because of the time out error on the server moscato1
Revision: 117797
Author: m.riester
Date: 2016-05-24T00:29:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/NAMESPACE
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_getSexFromCoverage.R
Fixed failing test.
Revision: 117795
Author: m.riester
Date: 2016-05-24T00:05:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Fixed new check warnings.
Revision: 117794
Author: m.riester
Date: 2016-05-24T00:00:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Modified  /trunk/madman/Rpacks/PureCN/man/plotAbs.Rd
Better transparency in BAF and AF.
Revision: 117792
Author: m.riester
Date: 2016-05-23T23:18:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Modified  /trunk/madman/Rpacks/PureCN/man/plotAbs.Rd
Removed default for transparency again, remove log-ratio outliers from the AF plot.
Revision: 117791
Author: m.jiang
Date: 2016-05-23T22:55:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
bump
Revision: 117789
Author: m.jiang
Date: 2016-05-23T22:55:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/src/include/transformation.hpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/macFlowJoWorkspace.cpp
parse caltbl as biexp for mac xml #203
Revision: 117788
Author: m.riester
Date: 2016-05-23T22:09:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/NAMESPACE
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Modified  /trunk/madman/Rpacks/PureCN/man/plotAbs.Rd
Added transparency to the allelic fraction plot.
Revision: 117785
Author: s.manimaran
Date: 2016-05-23T19:43:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/BatchQC/R/batchQC.R
Modified  /trunk/madman/Rpacks/BatchQC/inst/reports/batchqc_report.Rmd
Modified  /trunk/madman/Rpacks/BatchQC/inst/shiny/BatchQC/server.R
Consistently using lcounts which is either the log2CPM transformed or untransformed data based on the user provided option and keeping the default for log2CPM transformation as FALSE
Revision: 117784
Author: m.riester
Date: 2016-05-23T19:19:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Fixed typo.
Revision: 117783
Author: m.riester
Date: 2016-05-23T19:16:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/filterVcf.R
Modified  /trunk/madman/Rpacks/PureCN/R/getSex.R
Modified  /trunk/madman/Rpacks/PureCN/man/filterVcfBasic.Rd
Modified  /trunk/madman/Rpacks/PureCN/man/getSexFromCoverage.Rd
Modified  /trunk/madman/Rpacks/PureCN/man/getSexFromVcf.Rd
Modified  /trunk/madman/Rpacks/PureCN/man/runAbsoluteCN.Rd
Automatically add two diploid solutions with purity <0.5 and >0.5 to the local optima for noisy or very silent samples. Automatically determine good cutoff for minimum number of supporting reads based on coverage. Minor documentation improvements.
Revision: 117778
Author: s.hartley
Date: 2016-05-23T17:31:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/JunctionSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/JunctionSeq/LICENSE
Modified  /trunk/madman/Rpacks/JunctionSeq/NAMESPACE
Modified  /trunk/madman/Rpacks/JunctionSeq/NEWS
Modified  /trunk/madman/Rpacks/JunctionSeq/R/00.minor.utils.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/03.AllClasses.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/DESeq2.adapted.cpp.wrappers.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/adapted.functions.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/file.output.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/func.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/internal.func.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/main.analysis.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/main.plotAlt.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/main.plotGenes.R
Modified  /trunk/madman/Rpacks/JunctionSeq/R/plotting.helpers.R
Modified  /trunk/madman/Rpacks/JunctionSeq/man/buildAllPlots.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/buildAllPlotsForGene.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/defaultColorList.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/estimateEffectSizes.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/estimateJunctionSeqDispersions.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/estimateJunctionSeqSizeFactors.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/fitJunctionSeqDispersionFunction.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/plotDispEsts.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/plotJunctionSeqResultsForGene.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/plotMA.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/readAnnotationData.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/readJunctionSeqCounts.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/runJunctionSeqAnalyses.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/testForDiffUsage.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/writeBedTrack.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/man/writeCompleteResults.Rd
Modified  /trunk/madman/Rpacks/JunctionSeq/vignettes/JunctionSeq.Rnw
Modified  /trunk/madman/Rpacks/JunctionSeq/vignettes/JunctionSeq.bib
Updated to 1.3.4. Minor bug fixes
Revision: 117777
Author: p.blattmann
Date: 2016-05-23T15:37:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/SWATH2stats/DESCRIPTION
Modified  /trunk/madman/Rpacks/SWATH2stats/NEWS
Modified  /trunk/madman/Rpacks/SWATH2stats/R/sample_annotation.R
Modified  /trunk/madman/Rpacks/SWATH2stats/man/SWATH2stats-package.Rd
Modified  /trunk/madman/Rpacks/SWATH2stats/tests/testthat/test_loading.R
v.1.3.3: fail-safe for sample_annotation for non-unique file names

From: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Revision: 117773
Author: r.otto
Date: 2016-05-23T13:33:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/Uniquorn
Bug fix


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