diffloop: Identifying differential DNA loops from chromatin topology data
Version 1.4.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorCaleb Lareau [aut, cre], Martin Aryee [aut]
Bioconductor views DataImport DataRepresentation GO Preprocessing QualityControl Visualization
Date of publicationNone
MaintainerCaleb Lareau <caleblareau@g.harvard.edu>
LicenseMIT + file LICENSE
Version1.4.0
URL https://github.com/aryeelab/diffloop
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("diffloop")

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

[,loops,missing,numeric,missing-method Man page
[,loops,numeric,missing,missing-method Man page
[,loops,numeric,numeric,missing-method Man page
addchr Man page
addchr,GRanges-method Man page
addchr,loops-method Man page
annotateAnchors Man page Source code
annotateAnchors,loops,GRanges,character,missing-method Man page
annotateAnchors,loops,GRanges,character,numeric-method Man page
annotateAnchors.bed Man page
annotateAnchors.bed,ANY-method Man page
annotateAnchors.bigwig Man page
annotateAnchors.bigwig,ANY-method Man page
annotateLoops Man page
annotateLoops,loops,GRanges,GRanges,GRanges-method Man page
annotateLoops,loops,missing,GRanges,GRanges-method Man page
annotateLoops.dge Man page
annotateLoops.dge,ANY-method Man page
bedToGRanges Man page
bedToGRanges,character-method Man page
binmaker Source code
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
emptyloopsobject Source code
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
getHumanGenesNoCache Source code
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 Source code
loopPlot,loops,GRanges-method Man page
loopWidth Man page
loopWidth,loops-method Man page
loops Man page
loops-class Man page
loops.small Man page
loopsMake Man page Source code
loopsMake,ANY-method Man page
loopsMake.mango Man page Source code
loopsMake.mango,ANY-method Man page
loopsSubset Man page
loopsSubset,loops,loops-method Man page
makecombos Source code
mangoCorrection Man page
mangoCorrection,ANY-method Man page
manyLoopPlots Man page
manyLoopPlots,loops,GRanges-method Man page
mergeAnchors Man page Source code
mergeAnchors,loops,numeric,logical-method Man page
mergeAnchors,loops,numeric,missing-method Man page
model_chia Source code
numAnchors Man page
numAnchors,loops-method Man page
numLoops Man page Source code
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-method Man page
sampleNames<-,loops,ANY-method Man page
slidingWindowTest Man page
slidingWindowTest,loops,numeric,numeric-method Man page
splitSamples Man page
splitSamples,loops-method Man page
subsetLoops Man page Source code
subsetLoops,loops,logical-method Man page
subsetLoops,loops,numeric-method Man page
subsetRegion Man page
subsetRegion,loops,GRanges,missing-method Man page
subsetRegion,loops,GRanges,numeric-method Man page
subsetRegion1 Source code
subsetRegion2 Source code
subsetRegionAB Man page
subsetRegionAB,loops,GRanges,GRanges-method Man page
summary,loops-method Man page
tail,loops-method Man page
topLoops Man page Source code
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

.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R
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
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/diffloop.R
inst/doc/diffloop.Rmd
inst/doc/diffloop.html
inst/extdata
inst/extdata/Jurkat_CTCF_chr1.narrowPeak
inst/extdata/Jurkat_H3K27ac_chr1.narrowPeak
inst/extdata/chr1-TSS.bed
inst/rda
inst/rda/geneinfo.h.rda
inst/rda/geneinfo.m.rda
inst/rda/human.genes.rda
inst/rda/loops.small.rda
man
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
tests/testthat
tests/testthat.R
tests/testthat/test_diffloop.R
vignettes
vignettes/diffloop.Rmd
diffloop documentation built on May 20, 2017, 10:27 p.m.