chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Version 1.2.0

This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

Browse man pages Browse package API and functions Browse package files

AuthorAaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen
Bioconductor views ChIPSeq DifferentialPeakCalling HiddenMarkovModel HistoneModification MultipleComparison Software
Date of publicationNone
MaintainerAaron Taudt <aaron.taudt@gmail.com>
LicenseArtistic-2.0
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chromstaR")

Man pages

binned.data: Binned read counts
binReads: Convert aligned reads from various file formats into read...
callPeaksMultivariate: Fit a Hidden Markov Model to multiple ChIP-seq samples
callPeaksReplicates: Fit a multivariate Hidden Markov Model to multiple ChIP-seq...
callPeaksUnivariate: Fit a Hidden Markov Model to a ChIP-seq sample.
callPeaksUnivariateAllChr: Fit a Hidden Markov Model to a ChIP-seq sample.
changeFDR: Change the false discovery rate of a Hidden Markov Model
changePostCutoff: Change the posterior cutoff of a Hidden Markov Model
Chromstar: Wrapper function for the 'chromstaR' package
chromstaR-objects: chromstaR objects
chromstaR-package: Combinatorial and differential chromatin state analysis for...
collapseBins: Collapse consecutive bins
combinatorialStates: Get the (decimal) combinatorial states of a list of...
combined_model: Combined multivariate HMM for demonstration purposes
combinedMultiHMM: Combined multivariate HMM object
combineMultivariates: Combine combinatorial states from several Multivariates
conversion: Conversion of decimal and binary states
enrichment_analysis: Enrichment analysis
enrichmentAtAnnotation: Enrichment of (combinatorial) states for genomic annotations
experiment.table: Experiment data table
exportFiles: Export genome browser uploadable files
exportGRangesAsBedFile: Export genome browser viewable files
fixedWidthBins: Make fixed-width bins
genes_rn4: Gene coordinates for rn4
genomicFrequencies: Frequencies of combinatorial states
getCombinations: Get combinations
getDistinctColors: Get distinct colors
getStateColors: Get state colors
heatmapCombinations: Plot a heatmap of combinatorial states
heatmapCountCorrelation: Read count correlation heatmap
heatmapTransitionProbs: Heatmap of transition probabilities
loadHmmsFromFiles: Load 'chromstaR' objects from file
mergeChroms: Merge several 'multiHMM's into one object
multiHMM: Multivariate HMM object
multivariate_model: Multivariate HMM for demonstration purposes
multivariateSegmentation: Multivariate segmentation
plotExpression: Overlap with expression data
plotGenomeBrowser: Plot a genome browser view
plotHistogram: Histogram of binned read counts with fitted mixture...
plotHistograms: Histograms of binned read counts with fitted mixture...
plotKaryogram: Plot a karyogram with read counts and univariate peak calls
plotting: chromstaR plotting functions
print.combinedMultiHMM: Print combinedMultiHMM object
print.multiHMM: Print multiHMM object
print.uniHMM: Print uniHMM object
readBamFileAsGRanges: Import BAM file into GRanges
readBedFileAsGRanges: Import BED file into GRanges
readConfig: Read chromstaR configuration file
readCustomBedFile: Read bed-file into GRanges
removeCondition: Remove condition from model
scanBinsizes: Find the best bin size for a given dataset
scores: chromstaR scores
simulateMultivariate: Simulate multivariate data
simulateReadsFromCounts: Simulate read coordinates
simulateUnivariate: Simulate univariate data
state.brewer: Obtain combinatorial states from specification
stateBrewer: Obtain combinatorial states from experiment table
subsample: Normalize read counts
transitionFrequencies: Transition frequencies of combinatorial states
uniHMM: Univariate HMM object
unis2pseudomulti: Combine univariate HMMs to a multivariate HMM
variableWidthBins: Make variable-width bins
writeConfig: Write chromstaR configuration file
zinbinom: The Zero-inflated Negative Binomial Distribution

Functions

Chromstar Man page Source code
assignGroups Source code
bin2dec Man page Source code
binReads Man page Source code
binned.data Man page
binning Man page
callPeaksMultivariate Man page Source code
callPeaksReplicates Man page Source code
callPeaksUnivariate Man page Source code
callPeaksUnivariateAllChr Man page Source code
changeFDR Man page Source code
changeFDR.multivariate Source code
changeFDR.univariate Source code
changePostCutoff Man page Source code
changePostCutoff.multivariate Source code
changePostCutoff.univariate Source code
check.exclusive.table Source code
check.experiment.table Source code
check.integer Source code
check.logical Source code
check.multivariate.model Source code
check.multivariate.modellist Source code
check.nonnegative.integer Source code
check.nonnegative.integer.vector Source code
check.nonnegative.vector Source code
check.positive Source code
check.positive.integer Source code
check.positive.integer.vector Source code
check.positive.vector Source code
check.univariate.model Source code
check.univariate.modellist Source code
chromstaR Man page
chromstaR-objects Man page
chromstaR-package Man page
collapseBins Man page Source code
combinatorialStates Man page Source code
combineMultivariates Man page Source code
combinedHMM Man page
combinedMultiHMM Man page
combined_model Man page
conversion Man page
dec2bin Man page Source code
differentialScoreMax Man page Source code
differentialScoreSum Man page Source code
differentialScores Source code
dnbinom.mean Source code
dnbinom.prob Source code
dnbinom.size Source code
dnbinom.variance Source code
dzinbinom Man page Source code
enrichmentAtAnnotation Man page Source code
enrichment_analysis Man page
experiment.table Man page
exportBinnedData Source code
exportCombinations Man page Source code
exportCombinedMultivariate Source code
exportCombinedMultivariateCombinations Source code
exportCombinedMultivariateCounts Source code
exportCombinedMultivariatePeaks Source code
exportCounts Man page Source code
exportFiles Man page
exportGRangesAsBedFile Man page Source code
exportMultivariate Source code
exportMultivariateCombinations Source code
exportMultivariateCounts Source code
exportMultivariatePeaks Source code
exportPeaks Man page Source code
exportUnivariateCounts Source code
exportUnivariatePeaks Source code
exportUnivariates Source code
fixedWidthBins Man page Source code
genes_rn4 Man page
genomicFrequencies Man page Source code
getCombinations Man page Source code
getDistinctColors Man page Source code
getPeakScore.univariate Source code
getPeakScores Source code
getStateColors Man page Source code
get_rightxlim Source code
heatmapCombinations Man page Source code
heatmapCountCorrelation Man page Source code
heatmapTransitionProbs Man page Source code
insertchr Source code
loadHmmsFromFiles Man page Source code
mergeChroms Man page Source code
messageU Source code
multi.hmm Man page
multiHMM Man page
multivariateSegmentation Man page Source code
multivariate_model Man page
onAttach Source code
plotBoxplot Source code
plotEnrichCountHeatmap Man page Source code
plotEnrichment Man page Source code
plotExpression Man page Source code
plotFoldEnrichHeatmap Man page Source code
plotGenomeBrowser Man page Source code
plotHistogram Man page Source code
plotHistograms Man page Source code
plotKaryogram Man page Source code
plotNormalTransformation Source code
plotting Man page
prepareMultivariate Source code
print.combinedMultiHMM Man page Source code
print.multiHMM Man page Source code
print.uniHMM Man page Source code
pzinbinom Man page Source code
qzinbinom Man page Source code
readBamFileAsGRanges Man page Source code
readBedFileAsGRanges Man page Source code
readConfig Man page Source code
readCustomBedFile Man page Source code
removeCondition Man page Source code
rpkm.matrix Source code
rpkm.vector Source code
runMultivariate Source code
rzinbinom Man page Source code
scanBinsizes Man page Source code
scores Man page
simulateMultivariate Man page Source code
simulateReadsFromCounts Man page Source code
simulateUnivariate Man page Source code
startTimedMessage Source code
state.brewer Man page Source code
stateBrewer Man page Source code
stateorderByTransition Source code
stopTimedMessage Source code
subsample Man page Source code
transProbs Source code
transitionFrequencies Man page Source code
uni.hmm Man page
uniHMM Man page
unis2pseudomulti Man page Source code
variableWidthBins Man page Source code
writeConfig Man page Source code
zinbinom Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Chromstar.R
R/binReads.R
R/callPeaksMultivariate.R
R/callPeaksReplicates.R
R/callPeaksUnivariate.R
R/changeFDR.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/documented_plotting.R
R/enrichmentAnalysis.R
R/estimate.RAM.consumption.R
R/export.R
R/exportFiles.R
R/expressionAnalysis.R
R/frequencyAnalysis.R
R/getCombinations.R
R/getDistinctColors.R
R/global.R
R/importReads.R
R/loadHmmsFromFiles.R
R/makeBins.R
R/mergeChroms.R
R/peak_manipulation.R
R/plotting.R
R/printMethods.R
R/readCustomBedFile.R
R/removeCondition.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
build
build/vignette.rds
chromstaR_logo.png
chromstaR_logo.svg
data
data/combined_mode-differential.RData
data/datalist
data/genes_rn4.RData
data/multivariate_mode-combinatorial_condition-SHR.RData
inst
inst/CITATION
inst/doc
inst/doc/chromstaR.R
inst/doc/chromstaR.Rnw
inst/doc/chromstaR.pdf
man
man/Chromstar.Rd
man/binReads.Rd
man/binned.data.Rd
man/callPeaksMultivariate.Rd
man/callPeaksReplicates.Rd
man/callPeaksUnivariate.Rd
man/callPeaksUnivariateAllChr.Rd
man/changeFDR.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/combined_model.Rd
man/conversion.Rd
man/enrichmentAtAnnotation.Rd
man/enrichment_analysis.Rd
man/experiment.table.Rd
man/exportFiles.Rd
man/exportGRangesAsBedFile.Rd
man/fixedWidthBins.Rd
man/genes_rn4.Rd
man/genomicFrequencies.Rd
man/getCombinations.Rd
man/getDistinctColors.Rd
man/getStateColors.Rd
man/heatmapCombinations.Rd
man/heatmapCountCorrelation.Rd
man/heatmapTransitionProbs.Rd
man/loadHmmsFromFiles.Rd
man/mergeChroms.Rd
man/multiHMM.Rd
man/multivariateSegmentation.Rd
man/multivariate_model.Rd
man/plotExpression.Rd
man/plotGenomeBrowser.Rd
man/plotHistogram.Rd
man/plotHistograms.Rd
man/plotKaryogram.Rd
man/plotting.Rd
man/print.combinedMultiHMM.Rd
man/print.multiHMM.Rd
man/print.uniHMM.Rd
man/readBamFileAsGRanges.Rd
man/readBedFileAsGRanges.Rd
man/readConfig.Rd
man/readCustomBedFile.Rd
man/removeCondition.Rd
man/scanBinsizes.Rd
man/scores.Rd
man/simulateMultivariate.Rd
man/simulateReadsFromCounts.Rd
man/simulateUnivariate.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
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
tests/testthat
tests/testthat.R
tests/testthat/stateswap
tests/testthat/stateswap/H3K27Ac_GMP_Rep1_SRR1521798.bam_binsize_1000_chr_chr14.RData
tests/testthat/test_scores.R
tests/testthat/test_stateBrewer.R
tests/testthat/test_stateswap.R
vignettes
vignettes/chromstaR.Rnw
chromstaR documentation built on May 20, 2017, 9:40 p.m.