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 <>

DiffBind article

DiffBind citations

 (3)
2015
PMCID: 4973852

[…] each replicate were retained. peaks were retained for study only if they were observed in at least two independent replicates, using bedtools v.2.20.0 merge and intersect (quinlan and hall, 2010). diffbind v.1.12.0 (stark and brown, 2011) was used to perform correlation analyses of histone modifications., the rna‐seq data from the ibgsc (2012) project were used to divide gene transcripts […]

2015
PMCID: 4516306

[…] and fdr<0.01. the raw data file has been deposited to geo (s2 table)., dmr and dhmr identification are based on two independent methods. the first approach uses the r bioconductor package diffbind, which provides functions for processing chip-seq data enriched for genomic loci where specific protein/dna binding occurs, including peak-sets identified by chip-seq peak callers […]

2014
PMCID: 4039536

[…] [52]. called peaks were then cross-referenced against origins defined in oridb [53] as “confirmed” or “likely” to eliminate any peaks not aligning with an origin. origin peaks were subjected to diffbind analysis (fdr <0.05) for calling of differential peak sizes [54]. a final.txt file containing averaged data from the two experimental replicates was used for generating plots […]

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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