chromstaR-package | Combinatorial and differential chromatin state analysis for ChIP-seq data |
bin2dec | Conversion of decimal and binary states |
binned.data | Binned read counts |
binning | Convert aligned reads from various file formats into read counts in equidistant bins |
binReads | Convert aligned reads from various file formats into read counts in equidistant bins |
callPeaksMultivariate | Fit a Hidden Markov Model to multiple ChIP-seq samples |
callPeaksReplicates | Fit a multivariate Hidden Markov Model to multiple ChIP-seq replicates |
callPeaksUnivariate | Fit a Hidden Markov Model to a ChIP-seq sample. |
callPeaksUnivariateAllChr | Fit a Hidden Markov Model to a ChIP-seq sample. |
changeFDR | Change the false discovery rate of a Hidden Markov Model |
changePostCutoff | Change the posterior cutoff of a Hidden Markov Model |
Chromstar | Wrapper function for the 'chromstaR' package |
chromstaR | Combinatorial and differential chromatin state analysis for ChIP-seq data |
chromstaR-objects | chromstaR objects |
collapseBins | Collapse consecutive bins |
combinatorialStates | Get the (decimal) combinatorial states of a list of univariate HMM models |
combinedHMM | Combined multivariate HMM object |
combinedMultiHMM | Combined multivariate HMM object |
combined_model | Combined multivariate HMM for demonstration purposes |
combineMultivariates | Combine combinatorial states from several Multivariates |
conversion | Conversion of decimal and binary states |
dec2bin | Conversion of decimal and binary states |
differentialScoreMax | chromstaR scores |
differentialScoreSum | chromstaR scores |
dzinbinom | The Zero-inflated Negative Binomial Distribution |
enrichmentAtAnnotation | Enrichment of (combinatorial) states for genomic annotations |
enrichment_analysis | Enrichment analysis |
experiment.table | Experiment data table |
exportCombinations | Export genome browser uploadable files |
exportCounts | Export genome browser uploadable files |
exportFiles | Export genome browser uploadable files |
exportGRangesAsBedFile | Export genome browser viewable files |
exportPeaks | Export genome browser uploadable 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 |
multi.hmm | Multivariate HMM object |
multiHMM | Multivariate HMM object |
multivariateSegmentation | Multivariate segmentation |
multivariate_model | Multivariate HMM for demonstration purposes |
plotEnrichCountHeatmap | Enrichment analysis |
plotEnrichment | Enrichment analysis |
plotExpression | Overlap with expression data |
plotFoldEnrichHeatmap | Enrichment analysis |
plotGenomeBrowser | Plot a genome browser view |
plotHistogram | Histogram of binned read counts with fitted mixture distribution |
plotHistograms | Histograms of binned read counts with fitted mixture distribution |
plotKaryogram | Plot a karyogram with read counts and univariate peak calls |
plotting | chromstaR plotting functions |
print.combinedMultiHMM | Print combinedMultiHMM object |
print.multiHMM | Print multiHMM object |
print.uniHMM | Print uniHMM object |
pzinbinom | The Zero-inflated Negative Binomial Distribution |
qzinbinom | The Zero-inflated Negative Binomial Distribution |
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 |
rzinbinom | The Zero-inflated Negative Binomial Distribution |
scanBinsizes | Find the best bin size for a given dataset |
scores | chromstaR scores |
simulateMultivariate | Simulate multivariate data |
simulateReadsFromCounts | Simulate read coordinates |
simulateUnivariate | Simulate univariate 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 |
uni.hmm | Univariate HMM object |
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 |