Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Vignettes

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**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.**changeMaxPostCutoff:**Adjust sensitivity of peak detection**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...**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**model.combined:**Combined multivariate HMM for demonstration purposes**model.multivariate:**Multivariate HMM for demonstration purposes**model.univariate:**Univariate HMM for demonstration purposes**multiHMM:**Multivariate HMM object**multivariateSegmentation:**Multivariate segmentation**plotExpression:**Overlap with expression data**plotGenomeBrowser:**#' Plot a genome browser view #' #' Plot a simple genome...**plotHistogram:**Histogram of binned read counts with fitted mixture...**plotHistograms:**Histograms of binned read counts with fitted mixture...**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**Browse all...**

A `GRanges-class`

object which contains binned read counts as meta data column `counts`

. It is output of the `binReads`

function.

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