API for sojbaek/bagfootr
Bi-vAriate Genomic Footprinting (BaGFoot)
| Global functions | |
|---|---|
| CalcAggregationPerChromFastFixedWidthInC | Source code |
| CalcExpectedRates | Source code |
| CalcHeatmapFastFixedWidthC | Source code |
| CalcHeatmapFastMatrixOutputC | Source code |
| CalcObservedExpectedCuts | Source code |
| CalcSeqCodeForSeq | Source code |
| CompareHotspotsFaster | Source code |
| DrawStamMotifAggPlotOnChIPBoundRegions | Source code |
| FindSeqCodeInBase2ContainingSeqInBase1 | Source code |
| GFootSingleRun | Source code |
| MakeBiasCorrectionTableBAM | Man page Source code |
| MultipleAggregationPlot | Source code |
| OverlappingIndexAParallel | Source code |
| RunPairwiseComparison | Source code |
| ScatterDataOut | Source code |
| ScatterDataOutSingleRun | Source code |
| StamMotifAggPlot | Source code |
| basenameWithoutExt | Source code |
| bgr2rdensity | Source code |
| calcFrequencyTableBAMChromosome | Source code |
| col2ColorCode | Source code |
| combineTwoHotspots | Man page Source code |
| compare_intervals | Source code |
| convertBiasCorrectionTable | Source code |
| countCutcountOnSites | Source code |
| countReadsBAM | Source code |
| csv2bed | Source code |
| dlog | Source code Source code |
| drawMotifAggPlotOnMotifSets | Source code |
| drawMotifAggPlotOnMotifSetsForMultipleRangesAndWithComparisons | Source code |
| drawMotifAggPlotOnMotifSetsForMultipleRangesForSingleRun | Source code |
| extendHotspot | Source code |
| extractBaseName | Source code |
| file_check | Source code |
| filesizenotzero | Source code |
| filterHotspot | Source code |
| gen_bagplot | Source code |
| gen_bagplot_chisq | Source code |
| getDateStamp | Source code |
| getMaxLocBAM | Source code |
| getNucleotideString | Source code |
| getOutputDirAndFilename | Source code |
| intersect_intervals_fastInC | Source code |
| intersect_intervals_fast_index2C | Source code |
| intersect_intervals_fast_indexInC | Source code |
| intersect_intervals_fast_parallel | Source code |
| intersect_intervals_fast_parallel_index2 | Source code |
| intersect_intervals_really_fast_parallel | Source code |
| isBigEnough | Source code |
| loadChromosomeRange | Source code |
| loadReferenceGenome | Source code |
| load_global_options | Source code |
| makeCutCountBAM | Man page Source code |
| makeCutCountBAMWithName | Man page Source code |
| merge_two_frequency_tables | Source code |
| pickUnmappaleBasesByMappability | Source code |
| pool_hotspots3 | Source code |
| printf | Source code |
| quicksummaryListOrString | Source code |
| readBAMIndex | Source code |
| readCutCount | Source code |
| readCutCountOnSites | Source code |
| readCutSitesPerChromFromBAM | Source code |
| readFrequencyTable | Source code |
| readNucleotideCodeForChromosome | Source code |
| readNucleotideCodeForChromosomeForCuts | Source code |
| read_motif_file | Source code |
| readannot | Source code |
| readbed | Source code |
| readbed_as_csv | Source code |
| readbgr | Source code |
| readbgr2 | Source code |
| readcsv | Source code |
| readcsv2 | Source code |
| readcutcount2 | Source code |
| readcutcount3 | Source code |
| readhotspot | Source code |
| runGfoot | Source code |
| scatterDataOutGroups | Source code |
| scatterDataOutGroupsSingleRun | Source code |
| shiftarray | Source code |
| specialgrep | Source code |
| test_bagfoot_input | Source code |
| writeBGRHeader | Source code |
| writeBGRPerChrom | Source code |
| writeBGRheader | Source code |
| writeBGRperChromosomeR | Source code |
| writebed | Source code |
