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| binnedCoverage | binnedCoverage |
| computeZ | computeZ |
| constructBedRanges | constructBedRanges |
| countFinalRegions | countFinalRegions |
| createGranges | createGranges |
| cutGRangesPerChromosome | cutGRangesPerChromosome |
| DEScan2 | DEScan2 |
| divideEachSampleByChromosomes | divideEachSampleByChromosomes |
| finalRegions | finalRegions |
| findOverlapsOverSamples | findOverlapsOverSamples |
| findPeaks | findPeaks |
| fromSamplesToChrsGRangesList | fromSamplesToChrsGRangesList |
| keepRelevantChrs | keepRelevantChrs |
| readBamAsBed | readBamAsBed |
| readBedFile | readBedFile |
| readFilesAsGRangesList | readFilesAsGRangesList |
| RleListToRleMatrix | RleListToRleMatrix |
| saveGRangesAsBed | saveGRangesAsBed |
| saveGRangesAsTsv | saveGRangesAsTsv |
| setGRGenomeInfo | setGRGenomeInfo given a genome code (i.e. "mm9","mm10","hg19","hg38") retrieve the SeqInfo of that genome and assigns it to the input GRanges. Finally filters out those Infos not necessary to the GRanges. |