DiffBind: Differential Binding Analysis of ChIP-Seq peak data

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

Author
Rory Stark<rory.stark@cruk.cam.ac.uk>, Gord Brown <gdbzork@gmail.com>
Date of publication
None
Maintainer
Rory Stark<rory.stark@cruk.cam.ac.uk>
License
Artistic-2.0
Version
2.2.5

View on Bioconductor

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.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

Files in this package

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