Files in aryeelab/diffloop
Identifying differential DNA loops from chromatin topology data
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/annotation.R
R/assoc.R
R/colData.R
R/core.R
R/data.R
R/diffloop-class.R
R/diffloop.R
R/loopFunctions.R
R/mangoFunctions.R
R/pipeline_io.R
R/plotting.R
R/ruan.R
R/sugar.R
R/union.R
README.md
inst/NEWS.Rd
inst/extdata/Jurkat_CTCF_chr1.narrowPeak
inst/extdata/Jurkat_H3K27ac_chr1.narrowPeak
inst/extdata/chr1-TSS.bed
inst/rda/geneinfo.h.rda
inst/rda/geneinfo.m.rda
inst/rda/human.genes.rda
inst/rda/loops.small.rda
man/addchr.Rd
man/annotateAnchors.Rd
man/annotateAnchors.bed.Rd
man/annotateAnchors.bigwig.Rd
man/annotateLoops.Rd
man/annotateLoops.dge.Rd
man/bedToGRanges.Rd
man/calcLDSizeFactors.Rd
man/callCCDs.Rd
man/computeBoundaryScores.Rd
man/diffloop.Rd
man/dim-loops-method.Rd
man/featureTest.Rd
man/filterLoops.Rd
man/filterSpanningLoops.Rd
man/geneinfo.Rd
man/getHumanGenes.Rd
man/getHumanTSS.Rd
man/getMouseGenes.Rd
man/getMouseTSS.Rd
man/head-loops-method.Rd
man/human.genes.Rd
man/interchromosomal.Rd
man/intrachromosomal.Rd
man/keepCTCFloops.Rd
man/keepEPloops.Rd
man/loopAssoc.Rd
man/loopDistancePlot.Rd
man/loopGenes.Rd
man/loopMetrics.Rd
man/loopPlot.Rd
man/loopWidth.Rd
man/loops-class.Rd
man/loops.small.Rd
man/loopsMake.Rd
man/loopsMake.mango.Rd
man/loopsSubset.Rd
man/mangoCorrection.Rd
man/manyLoopPlots.Rd
man/mergeAnchors.Rd
man/numAnchors.Rd
man/numLoops.Rd
man/padGRanges.Rd
man/pcaPlot.Rd
man/plotTopLoops.Rd
man/quickAssoc.Rd
man/quickAssocVoom.Rd
man/removeRegion.Rd
man/removeSelfLoops.Rd
man/rmchr.Rd
man/sampleNames-loops-method.Rd
man/slidingWindowTest.Rd
man/splitSamples.Rd
man/sub-loops-numeric-numeric-missing-method.Rd
man/subsetLoops.Rd
man/subsetRegion.Rd
man/subsetRegionAB.Rd
man/summary-loops-method.Rd
man/tail-loops-method.Rd
man/topLoops.Rd
man/union-loops-loops-method.Rd
man/updateLDGroups.Rd
tests/testthat.R
tests/testthat/test_diffloop.R
vignettes/diffloop.Rmd
