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

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

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