API for Bioconductor-mirror/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_genomicRegions 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
getRAFfromgDNA Source code
getReport Source code
get_Vartable Source code
get_allele_counts Source code
get_average_stats Source code
get_filterstats 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
run_sim 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
Bioconductor-mirror/BaalChIP documentation built on May 29, 2017, 12:04 a.m.