DiffBind protocols

View DiffBind computational protocol

DiffBind statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Differential peak calling chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

DiffBind specifications

Information


Unique identifier OMICS_00471
Name DiffBind
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.8.0
Stability Stable
Requirements
limma, methods, stats, RColorBrewer, gplots, parallel, graphics, IRanges, GenomicRanges, Rsamtools, utils, testthat, S4Vectors, BiocStyle, grDevices, GenomicAlignments, R(>=3.5), SummarizedExperiment, amap, edgeR, locfit, zlibbioc, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, DESeq2, ggrepel, DESeq
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Rory Stark <>
  • person_outline Carlos Caldas <>
  • person_outline Jason Carroll <>

Publication for DiffBind

DiffBind in pipelines

 (29)
2018
PMCID: 5801776
PMID: 29409445
DOI: 10.1186/s12864-018-4509-0

[…] a poisson probability model to compare the observed read count to the expected read count and to compute a normalized peak score for each nucleotide position., dmrs were detected using the r package diffbind downloaded from the bioconductor repository (https://bioconductor.org/packages/release/bioc/html/diffbind.html), which computes differentially bound sites using affinity data. diffbind works […]

2018
PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] of peak datasets, (ii) occupancy analysis (for determining consensus peaksets) (iii) read counting (iv) differential binding affinity analysis and finally (v) plotting was conducted according to the diffbind protocol (). chip-seq peaks for tfbss were intersected within h3k4me3 peaks to ensure the analysis of actual promoter regions (). datasets for investigated tf were obtained via the geo; urls […]

2018
PMCID: 5834638
PMID: 29500414
DOI: 10.1038/s41419-018-0396-1

[…] version 1.3.1. alignment coordinates were converted to bed format using bedtools v.2.17 and h3k27ac peak calling was performed using sicer v1.1. differential h3k27ac binding was analyzed using the diffbind r/bioconductor package. the go term enrichment analysis was carried out on differentially bound (db) sites mapping in the tss regions with at least a two-fold change and fdr < 0.05 using […]

2018
PMCID: 5845016
PMID: 29523821
DOI: 10.1038/s41467-018-03417-3

[…] -l 32 --fr --local --maxins 1000 --minins 0). post-processing was done using sam tools (version 1.3.1). peaks were called using macs2 (version 2.1.1) with default parameters for human. afterwards a diffbind (version 2.0.6 with deseq2 1.12.4) analysis was performed to detect differentially bound regions for the control condition versus the uv condition. the peaks used for the analysis […]

2018
PMCID: 5849741
PMID: 29535300
DOI: 10.1038/s41467-018-03476-6

[…] significant peaks were then identified using the zero inflated negative binomial algorithm (zinba). resulting peak intensity information was combined with peak density data using diffbind to identify differential open chromatin sites between data derived from atrx- and atrx+ cell lines. novel genes with open chromatin regions were then annotated using annovar., tss/promoter […]


To access a full list of citations, you will need to upgrade to our premium service.

DiffBind in publications

 (100)
PMCID: 5953939
PMID: 29765031
DOI: 10.1038/s41467-018-04310-9

[…] that fall into peak regions, pcr bottleneck coefficient, normalized strand cross-correlation coefficient and the relative strand cross-correlation coefficient. chip-seq dmers were determined by diffbind package in r with q-value <0.05 for six marks., atac-seq sample preparation was followed by previous protocol and was sequenced by epinomics (san francisco, ca). atac-seq data […]

PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965

[…] and mod genes have been previously published [] and the raw data is available at geo (gse93871). chip-seq peak sets determined by macs2+idr method are found in . chip-seq peak sets using the macs2+diffbind method are found in . set of hic-5 blocked and non-blocked peaks are available in . open chromatin regions as determined by atac-seq are given in ., transcriptional regulation is a major […]

PMCID: 5922312
PMID: 29695303
DOI: 10.1186/s13059-018-1428-y

[…] subjected to the macs peak detection algorithm []. afterwards, peaks from the different samples were merged and quantified separately as fragments per kilobase per million reads (fpkm) using the diffbind package [], obtaining 27,310 peaks in control samples and 33,649 peaks in nabu samples, with 12,419 peaks shared by both conditions. finally, edger [] was applied to detect differential […]

PMCID: 5894188
PMID: 29636007
DOI: 10.1186/s12864-018-4548-6

[…] this software utilized a dynamic poisson distribution to effectively catch the local bias, improving the reliability of the prediction. after creating a contrast between conditions, the r package diffbind runs an edger analysis with a false discovery rate (fdr) < 0.1 to call the differentially methylated regions (dmrs). then, the chippeakanno package was used for the genomic annotation […]

PMCID: 5849741
PMID: 29535300
DOI: 10.1038/s41467-018-03476-6

[…] significant peaks were then identified using the zero inflated negative binomial algorithm (zinba). resulting peak intensity information was combined with peak density data using diffbind to identify differential open chromatin sites between data derived from atrx- and atrx+ cell lines. novel genes with open chromatin regions were then annotated using annovar., tss/promoter […]


To access a full list of publications, you will need to upgrade to our premium service.

DiffBind institution(s)
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK; UCL Cancer Institute, University College London, London, UK; Imperial College London, Hammersmith Campus, London, UK; Department of Gynaecology and Obstetrics, Third Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Histopathology, Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK; Department of Oncology, University of Cambridge, Cambridge, UK; Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Cambridge Experimental Cancer Medicine Centre (ECMC), Cambridge, UK
DiffBind funding source(s)
Supported by a Commonwealth Scholarship; by a grant awarded by the Ministry of Education of the Czech Republic (Project “Oncology” MSM 0021620808) and a Translational Research Fellow from the European Society of Medical Oncology; by CRUK and by an ERC starting grant and an EMBO Young investigator award.

DiffBind reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DiffBind