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

calculateBindingCharacteristicsGet binding characteristics
calculateIDRCalculate irreproducibly discovery rate
callPeaksCall peaks using SPP
encodeChIPqc-packageWhat the package does (short line) ~~ package title ~~
fripFraction of reads in peaks
gAlignmentsToSppTagsConvert GAlignments object to SPP tags
getCrossConsistencyRatiosGet cross-consistency ratios
getSelfConsistencyRatiosGet self-consistency ratios
IPstrengthPlot IP strength
mserAssess saturation properties
normalizeTagCountNormalize tag counts
PBCPCR bottleneck coefficient
pcaPlotPCA plot of ChIP and input samples
phantomPeakQC metrics RSC and NSC
plotIDRplot irreproducible discovery rate
samplesHeatmapHeatmap and cluster sample-sample distances
sppPeaksToGRangesConvert output from SPP to GRanges object
tagCountChIP-seq binned tag counting tool
topHeatmapHeatmap and cluster of top variant regions
imbforge/encodeChIPqc documentation built on May 17, 2017, 3:26 a.m.