Man pages for aryeelab/diffloop
Identifying differential DNA loops from chromatin topology data

addchrAdd 'chr' to GRanges seqnames
annotateAnchorsAdd meta data column to anchors based on GRanges
annotateAnchors.bedAdd meta data column to anchors based on bedgraph scores
annotateAnchors.bigwigAdd meta data column to anchors based on .bigwig
annotateLoopsAnnotate loops as Enhancer-Promoter or CTCF-CTCF
annotateLoops.dgeAnnotate enhancer-promoter loops with differential gene...
bedToGRangesRead a file and make a GRanges object
calcLDSizeFactorsCompute normalizing factors for each sample
callCCDsCompute Chromatin Contact Domains (CCDs)
computeBoundaryScoresCompute boundary scores for genomic loci in between anchors
diffloopdiffloop: A package for differential DNA loop calling from...
dim-loops-methodSee dimensions of loops object
featureTestCombined association test for all loops in a defined region
filterLoopsFilter loops
filterSpanningLoopsRetain loops spanning some genomic feature
geneinfoHuman/mouse exon locations
getHumanGenesGet protein coding gene regions
getHumanTSSGet Human Transcription Start Sites
getMouseGenesGet protein coding gene regions
getMouseTSSGet Mouse Transcription Start Sites
head-loops-methodExtract first part of loops object
human.genesHuman protein coding genes
interchromosomalLoops between chromosomes
intrachromosomalLoops within chromosomes
keepCTCFloopsKeep CTCF loops
keepEPloopsKeep enhancer-promoter loops
loopAssocGeneralized differential Loop Calling
loopDistancePlotVisualize proportion of loops at distances
loopGenesDetermine genes contained within loops
loopMetricsTypes of loops
loopPlotVisualize looping
loops-classA class to represent ChIA-PET interaction data and...
loopsMakeRead preprocessed ChIA-PET data from dnaloop
loopsMake.mangoRead preprocessed ChIA-PET data from mango
loops.smallchr1:36000000-36300000 loops
loopsSubsetSubset two difloop objects
loopWidthLoop widths
mangoCorrectionPerform mango bias correction
manyLoopPlotsPlot several loop regions
mergeAnchorsCombine nearby anchors into one peak
numAnchorsGet number of anchors in each sample
numLoopsPer-sample loop quantities
padGRangesPad a GRanges object
pcaPlotVisualize sample relationships
plotTopLoopsPlot the most significant loops
quickAssocPerform quick differential loop calling
quickAssocVoomPerform quick differential loop calling
removeRegionRemove region from loops object
removeSelfLoopsRemove self loops
rmchrRemove 'chr' from GRanges seqnames
sampleNames-loops-methodGrab/Update Sample Names
slidingWindowTestCombined association test for all loops in a defined region
splitSamplesSplit samples into their own loops object
sub-loops-numeric-numeric-missing-methodExtract parts of a loops object
subsetLoopsSubset loops
subsetRegionExtract region from loops object
subsetRegionABRetain loops that have anchors in two specified regions
summary-loops-methodLink the anchors and interactions back together
tail-loops-methodExtract last part of loops object
topLoopsGrab top loops
union-loops-loops-methodCombine two loops objects
updateLDGroupsUpdate groups in colData for loops object
aryeelab/diffloop documentation built on May 11, 2017, 2:13 a.m.