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 <firstname.lastname@example.org>|
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