Package: DiffBind 3.17.0

Rory Stark

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.

Authors:Rory Stark [aut, cre], Gord Brown [aut]

DiffBind_3.17.0.tar.gz
DiffBind_3.17.0.zip(r-4.5)DiffBind_3.17.0.zip(r-4.4)DiffBind_3.17.0.zip(r-4.3)
DiffBind_3.17.0.tgz(r-4.4-x86_64)DiffBind_3.17.0.tgz(r-4.3-x86_64)
DiffBind_3.17.0.tar.gz(r-4.5-noble)DiffBind_3.17.0.tar.gz(r-4.4-noble)
DiffBind.pdf |DiffBind.html✨
DiffBind/json (API)
NEWS

# Install 'DiffBind' in R:
install.packages('DiffBind', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:
  • tamoxifen - Tamoxifen resistance dataset used for DBA examples
  • tamoxifen - Tamoxifen resistance dataset used for DBA examples
  • tamoxifen - Tamoxifen resistance dataset used for DBA examples
  • tamoxifen.greylist - Tamoxifen resistance dataset used for DBA examples

On BioConductor:DiffBind-3.17.0(bioc 3.21)DiffBind-3.16.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencingchipseqatacseqdnaseseqmethylseqripseqdifferentialpeakcallingdifferentialmethylationgeneregulationhistonemodificationpeakdetectionbiomedicalinformaticscellbiologymultiplecomparisonnormalizationreportwritingepigeneticsfunctionalgenomicscurlbzip2xz-utilszlibcpp

7.08 score 2 packages 468 scripts 2.1k downloads 217 mentions 114 exports 138 dependencies

Last updated 2 months agofrom:67a8591187. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTENov 29 2024
R-4.4-mac-x86_64NOTENov 29 2024
R-4.3-win-x86_64NOTENov 29 2024
R-4.3-mac-x86_64NOTENov 29 2024

Exports:dbaDBA_ALL_ATTRIBUTESDBA_ALL_BLOCKDBA_ALL_METHODSDBA_ALL_METHODS_BLOCKDBA_BLACKLISTDBA_BLACKLIST_CE10DBA_BLACKLIST_CE11DBA_BLACKLIST_DM3DBA_BLACKLIST_DM6DBA_BLACKLIST_GRCH37DBA_BLACKLIST_GRCH38DBA_BLACKLIST_HG19DBA_BLACKLIST_HG38DBA_BLACKLIST_MM10DBA_BLACKLIST_MM9DBA_BLACKLISTED_PEAKSDBA_CALLERDBA_CONDITIONDBA_CONSENSUSDBA_CONTROLDBA_CORDBA_DATA_DBAOBJECTDBA_DATA_FRAMEDBA_DATA_GRANGESDBA_DATA_RANGEDDATADBA_DATA_SUMMARIZED_EXPERIMENTDBA_DESEQ2DBA_DESEQ2_BLOCKDBA_EDGERDBA_EDGER_BLOCKDBA_EDGER_GLMDBA_FACTORDBA_FRIPDBA_GREYLISTDBA_GROUPDBA_IDDBA_INALLDBA_INTERVALSDBA_LIBSIZE_BACKGROUNDDBA_LIBSIZE_DEFAULTDBA_LIBSIZE_FULLDBA_LIBSIZE_PEAKREADSDBA_LIBSIZE_USERDBA_NORM_DEFAULTDBA_NORM_LIBDBA_NORM_NATIVEDBA_NORM_OFFSETSDBA_NORM_OFFSETS_ADJUSTDBA_NORM_RLEDBA_NORM_SPIKEINDBA_NORM_TMMDBA_NORM_USERDBA_OFFSETS_LOESSDBA_OFFSETS_USERDBA_OLAPDBA_OLAP_ALLDBA_OLAP_PEAKSDBA_OLAP_RATEDBA_READSDBA_READS_BAMDBA_READS_BEDDBA_READS_DEFAULTDBA_REPLICATEDBA_SCORE_CONC_DENOMINATORDBA_SCORE_CONC_NUMERATORDBA_SCORE_CONCENTRATIONDBA_SCORE_CONTROL_READSDBA_SCORE_FDRDBA_SCORE_FOLDDBA_SCORE_NORMALIZEDDBA_SCORE_PVALDBA_SCORE_READSDBA_SCORE_READS_EFFECTIVEDBA_SCORE_READS_FOLDDBA_SCORE_READS_FULLDBA_SCORE_READS_MINUSDBA_SCORE_READS_MINUS_EFFECTIVEDBA_SCORE_READS_MINUS_FULLDBA_SCORE_RPKMDBA_SCORE_RPKM_FOLDDBA_SCORE_RPKM_MINUSDBA_SCORE_SUMMITDBA_SCORE_SUMMIT_ADJDBA_SCORE_SUMMIT_POSDBA_SCORE_TMM_MINUS_EFFECTIVEDBA_SCORE_TMM_MINUS_EFFECTIVE_CPMDBA_SCORE_TMM_MINUS_FULLDBA_SCORE_TMM_MINUS_FULL_CPMDBA_SCORE_TMM_READS_EFFECTIVEDBA_SCORE_TMM_READS_EFFECTIVE_CPMDBA_SCORE_TMM_READS_FULLDBA_SCORE_TMM_READS_FULL_CPMDBA_TISSUEDBA_TREATMENTdba.analyzedba.blacklistdba.contrastdba.countdba.loaddba.maskdba.normalizedba.overlapdba.peaksetdba.plotBoxdba.plotHeatmapdba.plotMAdba.plotPCAdba.plotProfiledba.plotVenndba.plotVolcanodba.reportdba.savedba.show

Dependencies:abindamapapeglmashraskpassbase64encbbmlebdsmatrixBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemcaToolsclicodacodetoolscolorspacecpp11crayoncurlDelayedArraydeldirDESeq2digestdplyremdbooketrunctevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggrepelgluegplotsGreyListChIPgtablegtoolshighrhtmltoolshtmlwidgetshttrhwriterinterpinvgammaIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelatticeExtralifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemixsqpmunsellmvtnormnlmenumDerivopensslpillarpkgconfigplyrpngpwalignR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsrtracklayerS4ArraysS4VectorssassscalesShortReadsnowSparseArraySQUAREMstatmodstringistringrSummarizedExperimentsyssystemPipeRtibbletidyselecttinytextruncnormUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzlibbioc

DiffBind: Differential binding analysis of ChIP-Seq peak data

Rendered fromDiffBind.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2022-10-04
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Differential Binding Analysis of ChIP-seq peaksetsDiffBind-package DiffBind
Construct a DBA objectdba
Standard S3 methods for DBA objectDBA-config DBA-object DBA.config DBA.object DiffBind-config DiffBind.config plot.DBA print.DBA summary.DBA
Tamoxifen resistance dataset used for DBA examplestamoxifen tamoxifen.greylist tamoxifen_analysis tamoxifen_counts tamoxifen_greylist tamoxifen_peaks
Perform differential binding affinity analysisdba.analyze
Apply blacklists and/or greylists to peaks (and generate greylist)dba.blacklist
Set up contrasts for differential binding affinity analysisdba.contrast
Count reads in binding site intervalsdba.count
load DBA objectdba.load
Derive a mask to define a subset of peaksets or sites for a DBA objectdba.mask
Specify parameters for normalizing a dataset; calculate library sizes and normalization factors.dba.normalize
Compute binding site overlaps (occupancy analysis)dba.overlap
Add a peakset to, or retrieve a peakset from, a DBA objectdba.peakset
Boxplotsdba.plotBox
Draw a binding site heatmapdba.plotHeatmap
Generate MA and scatter plots of differential binding analysis resultsdba.plotMA
PCA plotdba.plotPCA
Generate profiles and make profile heatmapsdba.plotProfile
Draw 2-way, 3-way, or 4-way Venn diagrams of overlapsdba.plotVenn
Generate volcano plots of differential binding analysis resultsdba.plotVolcano
Generate a report for a differential binding affinity analysisdba.report
save DBA objectdba.save
List attributes of peaksets of contrasts associated with a DBA objectdba.show
Constant variables used in DiffBind packageDBA_ALL_ATTRIBUTES DBA_ALL_BLOCK DBA_ALL_METHODS DBA_ALL_METHODS_BLOCK DBA_BLACKLIST DBA_BLACKLISTED_PEAKS DBA_BLACKLIST_CE10 DBA_BLACKLIST_CE11 DBA_BLACKLIST_DM3 DBA_BLACKLIST_DM6 DBA_BLACKLIST_GRCH37 DBA_BLACKLIST_GRCH38 DBA_BLACKLIST_HG19 DBA_BLACKLIST_HG38 DBA_BLACKLIST_MM10 DBA_BLACKLIST_MM9 DBA_CALLER DBA_CONDITION DBA_CONSENSUS DBA_CONTROL DBA_COR DBA_DATA_DBAOBJECT DBA_DATA_FRAME DBA_DATA_GRANGES DBA_DATA_RANGEDDATA DBA_DATA_SUMMARIZED_EXPERIMENT DBA_DESEQ2 DBA_DESEQ2_BLOCK DBA_EDGER DBA_EDGER_BLOCK DBA_EDGER_GLM DBA_FACTOR DBA_FRIP DBA_GREYLIST DBA_GROUP DBA_ID DBA_INALL DBA_INTERVALS DBA_LIBSIZE_BACKGROUND DBA_LIBSIZE_DEFAULT DBA_LIBSIZE_FULL DBA_LIBSIZE_PEAKREADS DBA_LIBSIZE_USER DBA_NORM_DEFAULT DBA_NORM_LIB DBA_NORM_NATIVE DBA_NORM_OFFSETS DBA_NORM_OFFSETS_ADJUST DBA_NORM_RLE DBA_NORM_SPIKEIN DBA_NORM_TMM DBA_NORM_USER DBA_OFFSETS_LOESS DBA_OFFSETS_USER DBA_OLAP DBA_OLAP_ALL DBA_OLAP_PEAKS DBA_OLAP_RATE DBA_READS DBA_READS_BAM DBA_READS_BED DBA_READS_DEFAULT DBA_REPLICATE DBA_SCORE_CONCENTRATION DBA_SCORE_CONC_DENOMINATOR DBA_SCORE_CONC_NUMERATOR DBA_SCORE_CONTROL_READS DBA_SCORE_FDR DBA_SCORE_FOLD DBA_SCORE_NORMALIZED DBA_SCORE_PVAL DBA_SCORE_READS DBA_SCORE_READS_EFFECTIVE DBA_SCORE_READS_FOLD DBA_SCORE_READS_FULL DBA_SCORE_READS_MINUS DBA_SCORE_READS_MINUS_EFFECTIVE DBA_SCORE_READS_MINUS_FULL DBA_SCORE_RPKM DBA_SCORE_RPKM_FOLD DBA_SCORE_RPKM_MINUS DBA_SCORE_SUMMIT DBA_SCORE_SUMMIT_ADJ DBA_SCORE_SUMMIT_POS DBA_SCORE_TMM_MINUS_EFFECTIVE DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM DBA_SCORE_TMM_MINUS_FULL DBA_SCORE_TMM_MINUS_FULL_CPM DBA_SCORE_TMM_READS_EFFECTIVE DBA_SCORE_TMM_READS_EFFECTIVE_CPM DBA_SCORE_TMM_READS_FULL DBA_SCORE_TMM_READS_FULL_CPM DBA_TISSUE DBA_TREATMENT
Differences between DiffBind 3.0 and earlier versionsDiffBind3