API for BaalChIP
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
| Global functions | |
|---|---|
| BaalChIP | Man page Source code |
| BaalChIP.checks | Source code |
| BaalChIP.get | Man page |
| BaalChIP.get,BaalChIP-method | Man page |
| BaalChIP.report | Man page |
| BaalChIP.report,BaalChIP-method | Man page |
| BaalChIP.run | Man page |
| BaalChIP.run,BaalChIP-method | Man page |
| BaalObject | Man page |
| Bayesian_report | Source code |
| ENCODEexample | Man page |
| FAIREexample | Man page |
| QCfilter | Man page |
| QCfilter,BaalChIP-method | Man page |
| Sum_read_counts | Source code |
| UniqueMappability50bp_hg19 | Man page |
| addVarTable | Source code |
| adjustmentBaalPlot | Man page |
| adjustmentBaalPlot,BaalChIP-method | Man page |
| alleleCounts | Man page |
| alleleCounts,BaalChIP-method | Man page |
| applyAlleleCountsPerBam | Source code |
| applyBayes | Source code |
| applyFilter1allele | Source code |
| applyFilteringStats | Source code |
| applyFiltersPerBam | Source code |
| applyIntBiasFilterPerBam | Source code |
| applyMergeResults | Source code |
| applyReadlenPerBam | Source code |
| applySim | Source code |
| bed2ranges | Source code |
| blacklist_hg19 | Man page |
| checkFileExists | Source code |
| checkmatchingnames | Source code |
| checkmatchingnames.gDNA | Source code |
| createtempdir | Source code |
| estimateRefBias | Source code |
| filter1allele | Man page |
| filter1allele,BaalChIP-method | Man page |
| filterIntbias | Man page |
| filterIntbias,BaalChIP-method | Man page |
| filter_1allele | Source code |
| filter_intbias | Source code |
| filter_regions | Source code |
| filter_sigi | Source code |
| getASB | Man page |
| getASB,BaalChIP-method | Man page |
| getBaalSlot | Source code |
| getMergedRepData | Source code |
| getReport | Source code |
| get_Vartable | Source code |
| get_allele_counts | Source code |
| get_average_stats | Source code |
| get_lastset | Source code |
| get_mergedcounts | Source code |
| get_readlen | Source code |
| get_simcounts | Source code |
| get_snp_ranges | Source code |
| get_snps_in_GI | Source code |
| getbiasTable | Source code |
| getbiasparam | Source code |
| getdframe | Source code |
| makeARGSTRING | Source code |
| mergePerGroup | Man page |
| mergePerGroup,BaalChIP-method | Man page |
| pickrell2011cov1_hg19 | Man page |
| plot.filt.barplot | Source code |
| plot.filt.boxplot | Source code |
| plot.filt.pie | Source code |
| plot.simul | Source code |
| plotQC | Man page |
| plotQC,BaalChIP-method | Man page |
| plotSimul | Man page |
| plotSimul,BaalChIP-method | Man page |
| plotadjustment | Source code |
| plotfilters | Source code |
| pooldata | Source code |
| readbams | Source code |
| readhettables | Source code |
| readsamplesheet | Source code |
| renameSeqlevels.allowNAs | Source code |
| runBayes | Source code |
| summaryASB | Man page |
| summaryASB,BaalChIP-method | Man page |
| summaryQC | Man page |
| summaryQC,BaalChIP-method | Man page |
| summary_ASB | Source code |
| summary_QC | Source code |
| tablenucs | Source code |
| trycreatedir | Source code |
| useRAFfromgDNA | Source code |
| useRAFfromhets | Source code |
