Files in diffloop

Identifying differential DNA loops from chromatin topology data

README.md R/diffloop-class.R R/core.R R/colData.R R/sugar.R R/mangoFunctions.R R/union.R R/pipeline_io.R R/plotting.R R/diffloop.R R/data.R R/ruan.R R/loopFunctions.R R/assoc.R R/annotation.R vignettes/diffloop.Rmd man/keepEPloops.Rd man/diffloop.Rd man/annotateLoops.dge.Rd man/numLoops.Rd man/getMouseGenes.Rd man/loopWidth.Rd man/removeSelfLoops.Rd man/summary-loops-method.Rd man/quickAssoc.Rd man/interchromosomal.Rd man/subsetRegionAB.Rd man/quickAssocVoom.Rd man/head-loops-method.Rd man/sub-loops-numeric-numeric-missing-method.Rd man/loopsMake.Rd man/mergeAnchors.Rd man/padGRanges.Rd man/dim-loops-method.Rd man/annotateLoops.Rd man/mangoCorrection.Rd man/computeBoundaryScores.Rd man/topLoops.Rd man/numAnchors.Rd man/featureTest.Rd man/loopDistancePlot.Rd man/addchr.Rd man/manyLoopPlots.Rd man/loopGenes.Rd man/intrachromosomal.Rd man/slidingWindowTest.Rd man/loops.small.Rd man/annotateAnchors.Rd man/getHumanGenes.Rd man/sampleNames-loops-method.Rd man/human.genes.Rd man/calcLDSizeFactors.Rd man/pcaPlot.Rd man/annotateAnchors.bed.Rd man/subsetLoops.Rd man/removeRegion.Rd man/tail-loops-method.Rd man/keepCTCFloops.Rd man/getHumanTSS.Rd man/loopPlot.Rd man/loopAssoc.Rd man/updateLDGroups.Rd man/getMouseTSS.Rd man/bedToGRanges.Rd man/callCCDs.Rd man/filterLoops.Rd man/loopsMake.mango.Rd man/subsetRegion.Rd man/geneinfo.Rd man/annotateAnchors.bigwig.Rd man/loops-class.Rd man/loopsSubset.Rd man/rmchr.Rd man/filterSpanningLoops.Rd man/loopMetrics.Rd man/plotTopLoops.Rd man/union-loops-loops-method.Rd man/splitSamples.Rd tests/testthat.R tests/testthat/test_diffloop.R inst/doc/diffloop.Rmd inst/doc/diffloop.R