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

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.

AuthorAaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen
Date of publicationNone
MaintainerAaron Taudt <aaron.taudt@gmail.com>
LicenseArtistic-2.0
Version1.0.0

View on Bioconductor

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.

changePostCutoff: Change the false discovery rate 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

exportBinnedData: Export genome browser viewable files

exportCombinedMultivariate: Export genome browser viewable files

exportGRangesAsBedFile: Export genome browser viewable files

exportMultivariate: Export genome browser viewable files

exportUnivariates: Export genome browser viewable files

fixedWidthBins: Make fixed-width bins

genomicFrequencies: Frequencies of combinatorial states

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

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

readBamFileAsGRanges: Import BAM file into GRanges

readBedFileAsGRanges: Import BED file into GRanges

readConfig: Read chromstaR configuration file

readCustomBedFile: Read bed-file into GRanges

scanBinsizes: Find the best bin size for a given dataset

scores: chromstaR scores

simulateReads: Simulate read coordinates

simulateUnivariate: Simulate 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

bin2dec Man page
binned.data Man page
binning Man page
binReads Man page
callPeaksMultivariate Man page
callPeaksReplicates Man page
callPeaksUnivariate Man page
callPeaksUnivariateAllChr Man page
changePostCutoff Man page
chromstaR Man page
Chromstar Man page
chromstaR-objects Man page
chromstaR-package Man page
collapseBins Man page
combinatorialStates Man page
combinedHMM Man page
combined_model Man page
combinedMultiHMM Man page
combineMultivariates Man page
conversion Man page
dec2bin Man page
differentialScoreMax Man page
differentialScoreSum Man page
dzinbinom Man page
enrichment_analysis Man page
enrichmentAtAnnotation Man page
experiment.table Man page
exportBinnedData Man page
exportCombinedMultivariate Man page
exportGRangesAsBedFile Man page
exportMultivariate Man page
exportUnivariates Man page
fixedWidthBins Man page
genomicFrequencies Man page
getDistinctColors Man page
getStateColors Man page
heatmapCombinations Man page
heatmapCountCorrelation Man page
heatmapTransitionProbs Man page
loadHmmsFromFiles Man page
mergeChroms Man page
multi.hmm Man page
multiHMM Man page
multivariate_model Man page
multivariateSegmentation Man page
plotEnrichCountHeatmap Man page
plotExpression Man page
plotFoldEnrichHeatmap Man page
plotFoldEnrichment Man page
plotHistogram Man page
plotHistograms Man page
plotKaryogram Man page
plotting Man page
pzinbinom Man page
qzinbinom Man page
readBamFileAsGRanges Man page
readBedFileAsGRanges Man page
readConfig Man page
readCustomBedFile Man page
rzinbinom Man page
scanBinsizes Man page
scores Man page
simulateReads Man page
simulateUnivariate Man page
state.brewer Man page
stateBrewer Man page
subsample Man page
transitionFrequencies Man page
uni.hmm Man page
uniHMM Man page
unis2pseudomulti Man page
variableWidthBins Man page
writeConfig Man page
zinbinom Man page

Files

chromstaR/DESCRIPTION
chromstaR/NAMESPACE
chromstaR/R
chromstaR/R/Chromstar.R chromstaR/R/bedimport.R chromstaR/R/binReads.R chromstaR/R/callPeaksMultivariate.R chromstaR/R/callPeaksReplicates.R chromstaR/R/callPeaksUnivariate.R chromstaR/R/changePostCutoff.R chromstaR/R/checkUserInput.R chromstaR/R/chromstaR-package.R chromstaR/R/collapseBins.R chromstaR/R/combinatorialStates.R chromstaR/R/combineMultivariates.R chromstaR/R/dec2bin.R chromstaR/R/documented_objects.R chromstaR/R/documented_plotting.R chromstaR/R/enrichment.plots.R chromstaR/R/enrichmentAnalysis.R chromstaR/R/estimate.RAM.consumption.R chromstaR/R/export.R chromstaR/R/expressionAnalysis.R chromstaR/R/frequencyAnalysis.R chromstaR/R/getDistinctColors.R chromstaR/R/global.R chromstaR/R/importReads.R chromstaR/R/loadHmmsFromFiles.R chromstaR/R/makeBins.R chromstaR/R/mergeChroms.R chromstaR/R/plotting.R chromstaR/R/rwConfig.R chromstaR/R/scanBinsizes.R chromstaR/R/scores.R chromstaR/R/segmentation.R chromstaR/R/simulate.R chromstaR/R/startup.R chromstaR/R/stateBrewer.R chromstaR/R/stateorderByTransition.R chromstaR/R/subsample.R chromstaR/R/summarize.R chromstaR/R/timedMessage.R chromstaR/R/unis2pseudomulti.R chromstaR/R/zinbinom.R
chromstaR/README.md
chromstaR/build
chromstaR/build/vignette.rds
chromstaR/chromstaR_logo.png
chromstaR/chromstaR_logo.svg
chromstaR/data
chromstaR/data/combined_mode-differential.RData
chromstaR/data/datalist
chromstaR/data/multivariate_mode-combinatorial_condition-SHR.RData
chromstaR/inst
chromstaR/inst/CITATION
chromstaR/inst/doc
chromstaR/inst/doc/chromstaR.R
chromstaR/inst/doc/chromstaR.Rnw
chromstaR/inst/doc/chromstaR.pdf
chromstaR/man
chromstaR/man/Chromstar.Rd chromstaR/man/binReads.Rd chromstaR/man/binned.data.Rd chromstaR/man/callPeaksMultivariate.Rd chromstaR/man/callPeaksReplicates.Rd chromstaR/man/callPeaksUnivariate.Rd chromstaR/man/callPeaksUnivariateAllChr.Rd chromstaR/man/changePostCutoff.Rd chromstaR/man/chromstaR-objects.Rd chromstaR/man/chromstaR-package.Rd chromstaR/man/collapseBins.Rd chromstaR/man/combinatorialStates.Rd chromstaR/man/combineMultivariates.Rd chromstaR/man/combinedMultiHMM.Rd chromstaR/man/combined_model.Rd chromstaR/man/conversion.Rd chromstaR/man/enrichmentAtAnnotation.Rd chromstaR/man/enrichment_analysis.Rd chromstaR/man/experiment.table.Rd chromstaR/man/exportBinnedData.Rd chromstaR/man/exportCombinedMultivariate.Rd chromstaR/man/exportGRangesAsBedFile.Rd chromstaR/man/exportMultivariate.Rd chromstaR/man/exportUnivariates.Rd chromstaR/man/fixedWidthBins.Rd chromstaR/man/genomicFrequencies.Rd chromstaR/man/getDistinctColors.Rd chromstaR/man/getStateColors.Rd chromstaR/man/heatmapCombinations.Rd chromstaR/man/heatmapCountCorrelation.Rd chromstaR/man/heatmapTransitionProbs.Rd chromstaR/man/loadHmmsFromFiles.Rd chromstaR/man/mergeChroms.Rd chromstaR/man/multiHMM.Rd chromstaR/man/multivariateSegmentation.Rd chromstaR/man/multivariate_model.Rd chromstaR/man/plotExpression.Rd chromstaR/man/plotHistogram.Rd chromstaR/man/plotHistograms.Rd chromstaR/man/plotKaryogram.Rd chromstaR/man/plotting.Rd chromstaR/man/readBamFileAsGRanges.Rd chromstaR/man/readBedFileAsGRanges.Rd chromstaR/man/readConfig.Rd chromstaR/man/readCustomBedFile.Rd chromstaR/man/scanBinsizes.Rd chromstaR/man/scores.Rd chromstaR/man/simulateReads.Rd chromstaR/man/simulateUnivariate.Rd chromstaR/man/state.brewer.Rd chromstaR/man/stateBrewer.Rd chromstaR/man/subsample.Rd chromstaR/man/transitionFrequencies.Rd chromstaR/man/uniHMM.Rd chromstaR/man/unis2pseudomulti.Rd chromstaR/man/variableWidthBins.Rd chromstaR/man/writeConfig.Rd chromstaR/man/zinbinom.Rd
chromstaR/src
chromstaR/src/Makevars
chromstaR/src/Makevars.win
chromstaR/src/R_interface.cpp
chromstaR/src/R_interface.h
chromstaR/src/densities.cpp
chromstaR/src/densities.h
chromstaR/src/init.cpp
chromstaR/src/logging.h
chromstaR/src/scalehmm.cpp
chromstaR/src/scalehmm.h
chromstaR/src/utility.cpp
chromstaR/src/utility.h
chromstaR/tests
chromstaR/tests/testthat
chromstaR/tests/testthat.R
chromstaR/tests/testthat/stateswap
chromstaR/tests/testthat/stateswap/H3K27Ac_GMP_Rep1_SRR1521798.bam_binsize_1000_chr_chr14.RData
chromstaR/tests/testthat/test_stateBrewer.R
chromstaR/tests/testthat/test_stateswap.R
chromstaR/vignettes
chromstaR/vignettes/chromstaR.Rnw

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