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corrected file permissions

chakalakka authored on 08/06/2016 09:00:02
Showing 121 changed files

.gitignore
DESCRIPTION
NAMESPACE
R/Chromstar.R
R/bedimport.R
R/binReads.R
R/callPeaksMultivariate.R
R/callPeaksReplicates.R
R/callPeaksUnivariate.R
R/changePostCutoff.R
R/checkUserInput.R
R/chromstaR-package.R
R/collapseBins.R
R/combinatorialStates.R
R/combineMultivariates.R
R/dec2bin.R
R/documented_objects.R
R/enrichment.plots.R
R/enrichmentAnalysis.R
R/estimate.RAM.consumption.R
R/export.R
R/expressionAnalysis.R
R/frequencyAnalysis.R
R/getDistinctColors.R
R/global.R
R/importReads.R
R/loadHmmsFromFiles.R
R/makeBins.R
R/mergeChroms.R
R/plotting.R
R/rwConfig.R
R/scanBinsizes.R
R/scores.R
R/segmentation.R
R/simulate.R
R/startup.R
R/stateBrewer.R
R/stateorderByTransition.R
R/subsample.R
R/summarize.R
R/timedMessage.R
R/unis2pseudomulti.R
R/zinbinom.R
README.md
data/multivariate_mode-mark_condition-SHR.RData
inst/CITATION
man/Chromstar.Rd
man/bam2GRanges.Rd
man/bed2GRanges.Rd
man/binReads.Rd
man/binned.data.Rd
man/callPeaksMultivariate.Rd
man/callPeaksReplicates.Rd
man/callPeaksUnivariate.Rd
man/callPeaksUnivariateAllChr.Rd
man/changePostCutoff.Rd
man/chromstaR-objects.Rd
man/chromstaR-package.Rd
man/collapseBins.Rd
man/combinatorialStates.Rd
man/combineMultivariates.Rd
man/combinedMultiHMM.Rd
man/conversion.Rd
man/differentialScoreMax.Rd
man/differentialScoreSum.Rd
man/enrichmentAtAnnotation.Rd
man/enrichment_analysis.Rd
man/experiment.table.Rd
man/exportBinnedData.Rd
man/exportCombinedMultivariate.Rd
man/exportGRanges.Rd
man/exportMultivariate.Rd
man/exportUnivariates.Rd
man/fixedWidthBins.Rd
man/genomicFrequencies.Rd
man/getDistinctColors.Rd
man/getStateColors.Rd
man/heatmapCombinations.Rd
man/importBed.Rd
man/loadHmmsFromFiles.Rd
man/mergeChroms.Rd
man/multiHMM.Rd
man/multivariateSegmentation.Rd
man/multivariate_model.Rd
man/plot.GRanges.Rd
man/plot.character.Rd
man/plot.multiHMM.Rd
man/plot.uniHMM.Rd
man/plotBinnedDataHistogram.Rd
man/plotExpression.Rd
man/plotUnivariateHistogram.Rd
man/plotUnivariateKaryogram.Rd
man/readConfig.Rd
man/scanBinsizes.Rd
man/state.brewer.Rd
man/stateBrewer.Rd
man/subsample.Rd
man/transitionFrequencies.Rd
man/uniHMM.Rd
man/unis2pseudomulti.Rd
man/variableWidthBins.Rd
man/writeConfig.Rd
man/zinbinom.Rd
src/Makevars
src/Makevars.win
src/R_interface.cpp
src/R_interface.h
src/densities.cpp
src/densities.h
src/init.cpp
src/logging.h
src/scalehmm.cpp
src/scalehmm.h
src/utility.cpp
src/utility.h
tests/testthat.R
tests/testthat/stateswap/H3K27Ac_GMP_Rep1_SRR1521798.bam_binsize_1000_chr_chr14.RData
tests/testthat/test_stateBrewer.R
tests/testthat/test_stateswap.R
vignettes/chromstaR.Rnw
vignettes/chromstaR.pdf

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DESCRIPTION

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NAMESPACE

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R/Chromstar.R

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R/bedimport.R

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R/binReads.R

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R/dec2bin.R

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R/estimate.RAM.consumption.R

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R/export.R

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R/expressionAnalysis.R

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R/global.R

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R/importReads.R

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R/loadHmmsFromFiles.R

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R/makeBins.R

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R/mergeChroms.R

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R/plotting.R

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R/rwConfig.R

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R/scores.R

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R/segmentation.R

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R/simulate.R

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R/startup.R

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R/stateBrewer.R

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R/timedMessage.R

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R/unis2pseudomulti.R

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R/zinbinom.R

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README.md

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data/multivariate_mode-mark_condition-SHR.RData

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inst/CITATION

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man/Chromstar.Rd

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man/bam2GRanges.Rd

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man/zinbinom.Rd

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src/Makevars

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src/Makevars.win

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src/init.cpp

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src/scalehmm.h

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tests/testthat.R

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tests/testthat/stateswap/H3K27Ac_GMP_Rep1_SRR1521798.bam_binsize_1000_chr_chr14.RData

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tests/testthat/test_stateswap.R

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vignettes/chromstaR.Rnw

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vignettes/chromstaR.pdf

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