Man pages for ibn-salem/chromloop
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

addCorAdd correlation of ChIP-seq coverage to motif pairs.
addCovCorAdd correlation of anchor signals to pairs of close genomic...
addCovToGRAdd coverage to regions in 'GRanges' object.
addInteractionSupportAdd column to 'GInteractions' with overlap support.
addMotifScoreAdd motif score of anchors.
addStrandCombinationAdd combination of anchor strand orientation.
cutoffBest10Default optimal cutoff value of logistic regression.
cutoffByTFOptimal cutoff values for logistic regression models.
getCisPairsBuild a 'GInteractions' object with all pairs of input...
getOutOfBoundGet out of chromosomal bound ranges.
modelBest10AvgDefault parameters for logistic regression model in sevenC.
motif.hg19.CTCFCTCF motif locations in human genome hg19.
motif.hg19.CTCF.chr22CTCF motif locations on chromosome 22 in human genome hg19.
motif.hg19.CTCF.chr22.covCTCF motifs on human chromosome 22 with example coverage.
noZeroVarreturns indices of columns with non-zero variance
parseLoopsRaoParse chromatin loops from Rao et al. 2014 as strict...
parseLoopsTang2015Parse chromatin interactions from Tang et al. 2015 as...
predLogitPredict interaction probability using logistic regression...
predLoopsPredict looping interactions.
prepareCisPairsPrepares motif pairs as 'GInteractions' and add genomic...
sevenCComputational chromosome conformation capture by correlation...
slideMeanSliding mean over x of intervals of size k
TFspecificModelsTF specific parameters for logistic regression in sevenC
ibn-salem/chromloop documentation built on Feb. 5, 2018, 11:35 p.m.