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.

Author
Aaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen
Date of publication
None
Maintainer
Aaron Taudt <aaron.taudt@gmail.com>
License
Artistic-2.0
Version
1.0.0

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

Files in this package

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