DiffBind protocols

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 2.6.6
Stability Stable
Requirements GenomicRanges, SummarizedExperiment, limma, GenomicAlignments, locfit
Maintained Yes

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Maintainers


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

Publication for DiffBind

DiffBind IN pipelines

 (8)
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 […]

2017
PMCID: 5442315
PMID: 28513600
DOI: 10.1038/ncomms15120

[…] out. consensus regions found as a sum of regions from two replications were taken as histone modification marks. differential modification analysis for h3k4me3 and h3k27me3 marks was performed using diffbind68 (bioconductor 3.2; minoverlap=2; fdr<0.01). the modification marks were intersected with annotated genes to obtain lists of genes with specific coverage by h3k4me3 and h3k27me3. […]

2017
PMCID: 5633079
PMID: 28825697
DOI: 10.1038/ncb3597

[…] (peaks) was performed using macs (version 2.0.10)56 with a p-value cut-off of 0.005 and the read counts were normalized against input sample. differential binding analysis was performed using the diffbind package (version 2.0.10)57., lsk cells isolated from the bm of pre-malignant mice were expanded in methocult m3434 methylcellulose medium (stemcell technologies). after 7 days colonies […]

2016
PMCID: 4960804
PMID: 27457071
DOI: 10.1186/s13059-016-1017-x

[…] for proliferating and senescent cells. the ratio of percentage mapped reads h4k20me3/percentage mapped reads control was then plotted., to determine the enrichment at te subtypes, for each set of diffbind peaks, the observed/expected fold overlap with each te subtype was calculated. te subtypes were obtained from ucsc. next, the evolutionary order of each te subtype was determined […]

2016
PMCID: 5030630
PMID: 27650712
DOI: 10.1038/srep33736

[…] was tested against the common for stimulated samples input dna obtained from one of the stimulated animals., peak detection was followed by differential binding analysis with r/bioconductor package diffbind 1.12.1 under r 3.1.2 software49. counts were normalized with trimmed mean of m-values (tmm) obtained with edger using chip read counts minus control read counts and full library size. mbd3 […]

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.

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