DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data
Version 2.4.2

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

AuthorRory Stark<rory.stark@cruk.cam.ac.uk>, Gord Brown <gdbzork@gmail.com>
Bioconductor views ChIPSeq DifferentialPeakCalling Sequencing
Date of publicationNone
MaintainerRory Stark<rory.stark@cruk.cam.ac.uk>
LicenseArtistic-2.0
Version2.4.2
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DiffBind")

Getting started

Package overview

Popular man pages

dba: Construct a DBA object
dba.analyze: Perform differential binding affinity analysis
dba.contrast: Set up contrasts for differential binding affinity analysis
dba.count: Count reads in binding site intervals
dba.peakset: Add a peakset to, or retrieve a peakset from, a DBA object
dba.plotVenn: Draw 2-way, 3-way, or 4-way Venn diagrams of overlaps
dba.report: Generate a report for a differential binding affinity...
See all...

All man pages Function index File listing

Man pages

dba: Construct a DBA object
dba.analyze: Perform differential binding affinity analysis
dba.contrast: Set up contrasts for differential binding affinity analysis
dba.count: Count reads in binding site intervals
dba.load: load DBA object
dba.mask: Derive a mask to define a subset of peaksets or sites for a...
dba.overlap: Compute binding site overlaps (occupancy analysis)
dba.peakset: Add a peakset to, or retrieve a peakset from, a DBA object
dba.plotBox: Boxplots
dba.plotHeatmap: Draw a binding site heatmap
dba.plotMA: Generate MA and scatter plots of differential binding...
dba.plotPCA: PCA plot
dba.plotVenn: Draw 2-way, 3-way, or 4-way Venn diagrams of overlaps
dba.plotVolcano: Generate volcano plots of differential binding analysis...
dba.report: Generate a report for a differential binding affinity...
dba.save: save DBA object
dba.show: List attributes of peaksets of contrasts associated with a...
DiffBind-globals: Constant variables used in DiffBind package
DiffBind-package: Differential Binding Analysis of ChIP-seq peaksets
print.DBA: Standard S3 methods for DBA object
tamoxifen: Tamoxifen resistance dataset used for DBA examples

Functions

Files

DESCRIPTION
NAMESPACE
R
R/DBA.R
R/RcppExports.R
R/analyze.R
R/contrast.R
R/core.R
R/counts.R
R/cpp_wrapper.R
R/helper.R
R/io.R
R/parallel.R
R/utils.R
build
build/vignette.rds
data
data/datalist
data/tamoxifen_analysis.rda
data/tamoxifen_counts.rda
data/tamoxifen_peaks.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/DiffBind.R
inst/doc/DiffBind.Rnw
inst/doc/DiffBind.pdf
inst/extra
inst/extra/config.csv
inst/extra/peaks
inst/extra/peaks/BT474_ER_1.bed.gz
inst/extra/peaks/BT474_ER_2.bed.gz
inst/extra/peaks/MCF7_ER_1.bed.gz
inst/extra/peaks/MCF7_ER_2.bed.gz
inst/extra/peaks/MCF7_ER_3.bed.gz
inst/extra/peaks/T47D_ER_1.bed.gz
inst/extra/peaks/T47D_ER_2.bed.gz
inst/extra/peaks/TAMR_ER_1.bed.gz
inst/extra/peaks/TAMR_ER_2.bed.gz
inst/extra/peaks/ZR75_ER_1.bed.gz
inst/extra/peaks/ZR75_ER_2.bed.gz
inst/extra/tamoxifen.csv
inst/extra/tamoxifen_GEO.R
inst/extra/tamoxifen_GEO.csv
inst/extra/tamoxifen_allfields.csv
inst/extra/testdata
inst/extra/testdata/bed_with_header.bed.gz
inst/extra/testdata/bed_without_header.bed.gz
inst/extra/testdata/raw_with_header.raw.gz
inst/extra/testdata/raw_without_header.raw.gz
inst/extra/testdata/test_sampleSheet_Spaces.csv
inst/extra/testdata/test_sampleSheet_Spaces.xlsx
inst/extra/testdata/test_sampleSheet_comment_char.csv
man
man/DiffBind-globals.Rd
man/DiffBind-package.Rd
man/dba.Rd
man/dba.analyze.Rd
man/dba.contrast.Rd
man/dba.count.Rd
man/dba.load.Rd
man/dba.mask.Rd
man/dba.overlap.Rd
man/dba.peakset.Rd
man/dba.plotBox.Rd
man/dba.plotHeatmap.Rd
man/dba.plotMA.Rd
man/dba.plotPCA.Rd
man/dba.plotVenn.Rd
man/dba.plotVolcano.Rd
man/dba.report.Rd
man/dba.save.Rd
man/dba.show.Rd
man/print.DBA.Rd
man/tamoxifen.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/bamReader.cpp
src/bamReader.h
src/bedReader.cpp
src/bedReader.h
src/bitBucket.cpp
src/bitBucket.h
src/croi_func.cpp
src/croi_func.h
src/croi_main.cpp
src/densitySet.cpp
src/densitySet.h
src/iBucket.cpp
src/iBucket.h
src/interval.cpp
src/interval.h
src/intervalDensity.cpp
src/intervalDensity.h
src/intervalNode.cpp
src/intervalNode.h
src/intervalSet.cpp
src/intervalSet.h
src/intervalTree.cpp
src/intervalTree.h
src/merge.cpp
src/mergeOne.c
src/nodeGroup.cpp
src/nodeGroup.h
src/peakOrder.cpp
src/reader.cpp
src/reader.h
src/sequence.cpp
src/sequence.h
src/util.cpp
src/util.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test_cmerge.R
tests/testthat/test_csort.R
tests/testthat/test_loadSampleSheet.R
tests/testthat/test_readPeaks.R
vignettes
vignettes/DiffBind.Rnw
vignettes/DiffBind.bib
DiffBind documentation built on May 20, 2017, 10:13 p.m.

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