diffloop: Identifying differential DNA loops from chromatin topology data

A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.

AuthorCaleb Lareau [aut, cre], Martin Aryee [aut]
Date of publicationNone
MaintainerCaleb Lareau <caleblareau@g.harvard.edu>
LicenseMIT + file LICENSE
Version1.2.2
https://github.com/aryeelab/diffloop

View on Bioconductor

Man pages

addchr: Add 'chr' to GRanges seqnames

annotateAnchors: Add meta data column to anchors based on GRanges

annotateAnchors.bed: Add meta data column to anchors based on bedgraph scores

annotateAnchors.bigwig: Add meta data column to anchors based on .bigwig

annotateLoops: Annotate loops as Enhancer-Promoter or CTCF-CTCF

annotateLoops.dge: Annotate enhancer-promoter loops with differential gene...

bedToGRanges: Read a file and make a GRanges object

calcLDSizeFactors: Compute normalizing factors for each sample

callCCDs: Compute Chromatin Contact Domains (CCDs)

computeBoundaryScores: Compute boundary scores for genomic loci in between anchors

diffloop: diffloop: A package for differential DNA loop calling from...

dim-loops-method: See dimensions of loops object

featureTest: Combined association test for all loops in a defined region

filterLoops: Filter loops

filterSpanningLoops: Retain loops spanning some genomic feature

geneinfo: Human/mouse exon locations

getHumanGenes: Get protein coding gene regions

getHumanTSS: Get Human Transcription Start Sites

getMouseGenes: Get protein coding gene regions

getMouseTSS: Get Mouse Transcription Start Sites

head-loops-method: Extract first part of loops object

human.genes: Human protein coding genes

interchromosomal: Loops between chromosomes

intrachromosomal: Loops within chromosomes

keepCTCFloops: Keep CTCF loops

keepEPloops: Keep enhancer-promoter loops

loopAssoc: Generalized differential Loop Calling

loopDistancePlot: Visualize proportion of loops at distances

loopGenes: Determine genes contained within loops

loopMetrics: Types of loops

loopPlot: Visualize looping

loops-class: A class to represent ChIA-PET interaction data and...

loopsMake: Read preprocessed ChIA-PET data from dnaloop

loopsMake.mango: Read preprocessed ChIA-PET data from mango

loops.small: chr1:36000000-36300000 loops

loopsSubset: Subset two difloop objects

loopWidth: Loop widths

mangoCorrection: Perform mango bias correction

manyLoopPlots: Plot several loop regions

mergeAnchors: Combine nearby anchors into one peak

numAnchors: Get number of anchors in each sample

numLoops: Per-sample loop quantities

padGRanges: Pad a GRanges object

pcaPlot: Visualize sample relationships

plotTopLoops: Plot the most significant loops

quickAssoc: Perform quick differential loop calling

quickAssocVoom: Perform quick differential loop calling

removeRegion: Remove region from loops object

removeSelfLoops: Remove self loops

rmchr: Remove 'chr' from GRanges seqnames

sampleNames-loops-method: Grab/Update Sample Names

slidingWindowTest: Combined association test for all loops in a defined region

splitSamples: Split samples into their own loops object

sub-loops-numeric-numeric-missing-method: Extract parts of a loops object

subsetLoops: Subset loops

subsetRegion: Extract region from loops object

subsetRegionAB: Retain loops that have anchors in two specified regions

summary-loops-method: Link the anchors and interactions back together

tail-loops-method: Extract last part of loops object

topLoops: Grab top loops

union-loops-loops-method: Combine two loops objects

updateLDGroups: Update groups in colData for loops object

Functions

addchr Man page
addchr,GRanges-method Man page
addchr,loops-method Man page
annotateAnchors Man page
annotateAnchors.bed Man page
annotateAnchors.bed,ANY-method Man page
annotateAnchors.bigwig Man page
annotateAnchors.bigwig,ANY-method Man page
annotateAnchors,loops,GRanges,character,missing-method Man page
annotateAnchors,loops,GRanges,character,numeric-method Man page
annotateLoops Man page
annotateLoops.dge Man page
annotateLoops.dge,ANY-method Man page
annotateLoops,loops,GRanges,GRanges,GRanges-method Man page
annotateLoops,loops,missing,GRanges,GRanges-method Man page
bedToGRanges Man page
bedToGRanges,character-method Man page
calcLDSizeFactors Man page
calcLDSizeFactors,loops-method Man page
callCCDs Man page
callCCDs,ANY-method Man page
computeBoundaryScores Man page
computeBoundaryScores,loops-method Man page
diffloop Man page
diffloop-package Man page
dim,loops-method Man page
featureTest Man page
featureTest,loops,GRanges-method Man page
filterLoops Man page
filterLoops,ANY-method Man page
filterSpanningLoops Man page
filterSpanningLoops,loops,GRanges-method Man page
geneinfo Man page
getHumanGenes Man page
getHumanGenes,character-method Man page
getHumanGenes,missing-method Man page
getHumanTSS Man page
getHumanTSS,character-method Man page
getHumanTSS,missing-method Man page
getMouseGenes Man page
getMouseGenes,character-method Man page
getMouseGenes,missing-method Man page
getMouseTSS Man page
getMouseTSS,character-method Man page
getMouseTSS,missing-method Man page
head,loops-method Man page
human.genes Man page
interchromosomal Man page
interchromosomal,loops-method Man page
intrachromosomal Man page
intrachromosomal,loops-method Man page
keepCTCFloops Man page
keepCTCFloops,loops,GRanges-method Man page
keepEPloops Man page
keepEPloops,loops,GRanges,GRanges-method Man page
loopAssoc Man page
loopAssoc,loops-method Man page
loopDistancePlot Man page
loopDistancePlot,loops-method Man page
loopGenes Man page
loopGenes,loops,GRanges-method Man page
loopGenes,loops,missing-method Man page
loopMetrics Man page
loopMetrics,loops-method Man page
loopPlot Man page
loopPlot,loops,GRanges-method Man page
loops Man page
loops-class Man page
loopsMake Man page
loopsMake,ANY-method Man page
loopsMake.mango Man page
loopsMake.mango,ANY-method Man page
[,loops,missing,numeric,missing-method Man page
[,loops,numeric,missing,missing-method Man page
[,loops,numeric,numeric,missing-method Man page
loops.small Man page
loopsSubset Man page
loopsSubset,loops,loops-method Man page
loopWidth Man page
loopWidth,loops-method Man page
mangoCorrection Man page
mangoCorrection,ANY-method Man page
manyLoopPlots Man page
manyLoopPlots,loops,GRanges-method Man page
mergeAnchors Man page
mergeAnchors,loops,numeric,logical-method Man page
mergeAnchors,loops,numeric,missing-method Man page
numAnchors Man page
numAnchors,loops-method Man page
numLoops Man page
numLoops,loops,missing-method Man page
numLoops,loops,numeric-method Man page
padGRanges Man page
padGRanges,GRanges-method Man page
pcaPlot Man page
pcaPlot,loops-method Man page
plotTopLoops Man page
plotTopLoops,loops-method Man page
quickAssoc Man page
quickAssoc,loops-method Man page
quickAssocVoom Man page
quickAssocVoom,loops-method Man page
removeRegion Man page
removeRegion,loops,GRanges-method Man page
removeSelfLoops Man page
removeSelfLoops,loops-method Man page
rmchr Man page
rmchr,GRanges-method Man page
rmchr,loops-method Man page
sampleNames<-,loops,ANY-method Man page
sampleNames,loops-method Man page
slidingWindowTest Man page
slidingWindowTest,loops,numeric,numeric-method Man page
splitSamples Man page
splitSamples,loops-method Man page
subsetLoops Man page
subsetLoops,loops,logical-method Man page
subsetLoops,loops,numeric-method Man page
subsetRegion Man page
subsetRegionAB Man page
subsetRegionAB,loops,GRanges,GRanges-method Man page
subsetRegion,loops,GRanges,missing-method Man page
subsetRegion,loops,GRanges,numeric-method Man page
summary,loops-method Man page
tail,loops-method Man page
topLoops Man page
topLoops,loops,missing,numeric-method Man page
topLoops,loops,numeric,missing-method Man page
topLoops,loops,numeric,numeric-method Man page
union,loops,loops-method Man page
updateLDGroups Man page
updateLDGroups,loops-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.