API for imbforge/encodeChIPqc
A set of useful ChIPseq QC metrics from the ENCODE project

Global functions
IPstrength Man page Source code
PBC Man page Source code
calculateBindingCharacteristics Man page Source code
calculateIDR Man page Source code
callPeaks Man page Source code
clayton.cop.den Source code
clean.data Source code
clusterApplyLB Source code
comp.ez.cutoff Source code
comp.uri Source code
comp.uri.ez Source code
compute.pair.uri Source code
concatenate.chr Source code
d.binormal Source code
deconcatenate.chr Source code
e.step.2copula Source code
e.step.2copula.value Source code
e.step.2gaussian Source code
e.step.2gaussian.value Source code
e.step.2normal Source code
em.2copula.quick Source code
em.2gaussian.quick Source code
em.transform Source code
encodeChIPqc Man page
encodeChIPqc-package Man page
est.cdf.rank Source code
est.mar.hist Source code
fill.missing.peaks Source code
find.mu.sigma Source code
find.overlap Source code
find.peaks Source code
fit.1.component Source code
fit.2copula.em Source code
fit.clayton.1 Source code
fit.em Source code
fit.gaussian.1 Source code
frip Man page Source code
gAlignmentsToSppTags Man page Source code
gaussian.cop.den Source code
get.cdf Source code
get.ez Source code
get.ez.tt Source code
get.ez.tt.all Source code
get.hist.mean Source code
get.hist.var Source code
get.mar.mean Source code
get.pdf Source code
get.pdf.cdf Source code
get.pseudo.mix Source code
get.uri.2d Source code
get.uri.matched Source code
getCrossConsistencyRatios Man page Source code
getSelfConsistencyRatios Man page Source code
init Source code
init.dist Source code
loglik.2binormal Source code
loglik.2copula Source code
loglik.2copula.value Source code
loglik.2gaussian.copula Source code
loglik.2gaussian.copula.value Source code
m.step.2copula Source code
m.step.2copula.value Source code
m.step.2gaussian Source code
m.step.2gaussian.value Source code
m.step.2gaussian.value2 Source code
m.step.2normal Source code
map.sig.value Source code
merge.peaks Source code
merge.peaks.best Source code
mle.clayton.copula Source code
mle.gaussian.copula Source code
mser Man page Source code
normalizeTagCount Man page Source code
overlap.middle Source code
pair.peaks Source code
pair.peaks.filter Source code
pcaPlot Man page Source code
phantomPeak Man page Source code
plot.ez.group Source code
plot.uri.group Source code
plotIDR Man page Source code
process.narrowpeak Source code
rm.unmatch Source code
samplesHeatmap Man page Source code
scale.t2n Source code
sppPeaksToGRanges Man page Source code
tagCount Man page Source code
topHeatmap Man page Source code
imbforge/encodeChIPqc documentation built on May 17, 2017, 3:26 a.m.