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.

AuthorRory Stark<rory.stark@cruk.cam.ac.uk>, Gord Brown <gdbzork@gmail.com>
Date of publicationNone
MaintainerRory Stark<rory.stark@cruk.cam.ac.uk>
LicenseArtistic-2.0
Version2.2.8

View on Bioconductor

Functions

dba Man page
DBA Man page
DBA_ALL_ATTRIBUTES Man page
DBA_ALL_BLOCK Man page
DBA_ALL_METHODS Man page
DBA_ALL_METHODS_BLOCK Man page
dba.analyze Man page
DBA_CALLER Man page
DBA_CONDITION Man page
DBA_CONSENSUS Man page
dba.contrast Man page
DBA_CONTROL Man page
DBA_COR Man page
dba.count Man page
DBA_DATA_DBAOBJECT Man page
DBA_DATA_FRAME Man page
DBA_DATA_GRANGES Man page
DBA_DATA_RANGEDDATA Man page
DBA_DATA_SUMMARIZED_EXPERIMENT Man page
DBA_DESEQ Man page
DBA_DESEQ2 Man page
DBA_DESEQ2_BLOCK Man page
DBA_DESEQ_BLOCK Man page
DBA_DESEQ_CLASSIC Man page
DBA_DESEQ_GLM Man page
DBA_EDGER Man page
DBA_EDGER_BLOCK Man page
DBA_EDGER_CLASSIC Man page
DBA_EDGER_GLM Man page
DBA_FACTOR Man page
DBA_FRIP Man page
DBA_GROUP Man page
DBA_ID Man page
DBA_INALL Man page
DBA_INTERVALS Man page
dba.load Man page
dba.mask Man page
DBA_OLAP Man page
DBA_OLAP_ALL Man page
DBA_OLAP_PEAKS Man page
DBA_OLAP_RATE Man page
dba.overlap Man page
dba.peakset Man page
dba.plotBox Man page
dba.plotHeatmap Man page
dba.plotMA Man page
dba.plotPCA Man page
dba.plotVenn Man page
DBA_READS_BAM Man page
DBA_READS_BED Man page
DBA_READS_DEFAULT Man page
DBA_REPLICATE Man page
dba.report Man page
dba.save Man page
DBA_SCORE_READS Man page
DBA_SCORE_READS_FOLD Man page
DBA_SCORE_READS_MINUS Man page
DBA_SCORE_RPKM Man page
DBA_SCORE_RPKM_FOLD Man page
DBA_SCORE_SUMMIT Man page
DBA_SCORE_SUMMIT_ADJ Man page
DBA_SCORE_SUMMIT_POS Man page
DBA_SCORE_TMM_MINUS_EFFECTIVE Man page
DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM Man page
DBA_SCORE_TMM_MINUS_FULL Man page
DBA_SCORE_TMM_MINUS_FULL_CPM Man page
DBA_SCORE_TMM_READS_EFFECTIVE Man page
DBA_SCORE_TMM_READS_EFFECTIVE_CPM Man page
DBA_SCORE_TMM_READS_FULL Man page
DBA_SCORE_TMM_READS_FULL_CPM Man page
dba.show Man page
DBA_TISSUE Man page
DBA_TREATMENT Man page
DiffBind Man page
DiffBind-package Man page
plot.DBA Man page
print.DBA Man page
summary.DBA Man page
tamoxifen Man page
tamoxifen_analysis Man page
tamoxifen_counts Man page
tamoxifen_peaks Man page

Files

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

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