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.

Author
Caleb Lareau [aut, cre], Martin Aryee [aut]
Date of publication
None
Maintainer
Caleb Lareau <caleblareau@g.harvard.edu>
License
MIT + file LICENSE
Version
1.2.1
URLs

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

Files in this package

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