1 Introduction | 2 Processing overview | 3 Example: Obtaining differentially bound sites | 4 Plotting in DiffBind | 5 Example: Multi-factor designs | 6 Blacklists and Greylists | 7 Normalization | 8 Example: Occupancy analysis and overlaps | 9 Backward compatibility with pre-version 3.0 analyses | 10 Technical notes | 11 Technical notes for versions prior to DiffBind 3.0 (without an explicit model design) | 12 Vignette Data | 13 Using DiffBind and ChIPQC together | 14 Acknowledgements | 15 Session Info
Package: DiffBind 3.23.3
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:
DiffBind_3.23.3.tar.gz
DiffBind_3.23.3.zip(r-4.7)DiffBind_3.23.3.zip(r-4.6)DiffBind_3.23.3.zip(r-4.5)
DiffBind_3.23.3.tgz(r-4.6-x86_64)DiffBind_3.23.3.tgz(r-4.6-arm64)DiffBind_3.23.3.tgz(r-4.5-x86_64)DiffBind_3.23.3.tgz(r-4.5-arm64)
DiffBind_3.23.3.tar.gz(r-4.7-arm64)DiffBind_3.23.3.tar.gz(r-4.7-x86_64)DiffBind_3.23.3.tar.gz(r-4.6-arm64)DiffBind_3.23.3.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DiffBind/json (API)
| # Install 'DiffBind' in R: |
| install.packages('DiffBind', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Uses libs:
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-3.23.2(bioc 3.24)DiffBind-3.22.1(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingchipseqatacseqdnaseseqmethylseqripseqdifferentialpeakcallingdifferentialmethylationgeneregulationhistonemodificationpeakdetectionbiomedicalinformaticscellbiologymultiplecomparisonnormalizationreportwritingepigeneticsfunctionalgenomicscurlbzip2xz-utilszlibcpp
Last updated from:a26ef8d38f. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 206 | ||
| linux-devel-arm64 | WARNING | 542 | ||
| linux-devel-x86_64 | WARNING | 631 | ||
| source / vignettes | OK | 468 | ||
| linux-release-arm64 | WARNING | 517 | ||
| linux-release-x86_64 | WARNING | 630 | ||
| macos-release-arm64 | WARNING | 358 | ||
| macos-release-x86_64 | WARNING | 641 | ||
| macos-oldrel-arm64 | WARNING | 361 | ||
| macos-oldrel-x86_64 | WARNING | 738 | ||
| windows-devel | WARNING | 691 | ||
| windows-release | WARNING | 646 | ||
| windows-oldrel | WARNING | 666 | ||
| wasm-release | FAIL | 219 |
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:abindamapapeglmashraskpassbase64encbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemcaToolscigarilloclicodacodetoolscpp11crayoncurlDelayedArraydeldirDESeq2digestdplyremdbooketrunctevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggrepelgluegplotsGreyListChIPgtablegtoolshighrhtmltoolshtmlwidgetshttrhwriterinterpinvgammaIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelatticeExtralifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemixsqpmvtnormnumDerivopensslpillarpkgconfigplyrpngpwalignR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsrtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoShortReadsnowSparseArraySQUAREMstatmodstringistringrSummarizedExperimentsyssystemPipeRtibbletidyselecttinytextruncnormutf8vctrsviridisLitewithrxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Differential Binding Analysis of ChIP-seq peaksets | DiffBind-package DiffBind |
| Construct a DBA object | dba |
| Standard S3 methods for DBA object | DBA-config DBA-object DBA.config DBA.object DiffBind-config DiffBind.config plot.DBA print.DBA summary.DBA |
| Tamoxifen resistance dataset used for DBA examples | tamoxifen tamoxifen.greylist tamoxifen_analysis tamoxifen_counts tamoxifen_greylist tamoxifen_peaks |
| Perform differential binding affinity analysis | dba.analyze |
| Apply blacklists and/or greylists to peaks (and generate greylist) | dba.blacklist |
| Set up contrasts for differential binding affinity analysis | dba.contrast |
| Count reads in binding site intervals | dba.count |
| load DBA object | dba.load |
| Derive a mask to define a subset of peaksets or sites for a DBA object | dba.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 object | dba.peakset |
| Boxplots | dba.plotBox |
| Draw a binding site heatmap | dba.plotHeatmap |
| Generate MA and scatter plots of differential binding analysis results | dba.plotMA |
| PCA plot | dba.plotPCA |
| Generate profiles and make profile heatmaps | dba.plotProfile |
| Draw 2-way, 3-way, or 4-way Venn diagrams of overlaps | dba.plotVenn |
| Generate volcano plots of differential binding analysis results | dba.plotVolcano |
| Generate a report for a differential binding affinity analysis | dba.report |
| save DBA object | dba.save |
| List attributes of peaksets of contrasts associated with a DBA object | dba.show |
| Constant variables used in DiffBind package | DBA_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 versions | DiffBind3 |