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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 2.8.0
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

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Versioning


No version available

Documentation


Maintainers


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

Publication for DiffBind

DiffBind citations

 (111)
library_books

Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast like synoviocytes

2018
Nat Commun
PMCID: 5953939
PMID: 29765031
DOI: 10.1038/s41467-018-04310-9

[…] reads 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. […]

call_split

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic 5

2018
PLoS One
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965
call_split See protocol

[…] -Seq version 2 (MACS2) [] and the Irreproducibility Discovery Rate (IDR) framework developed for ENCODE [https://sites.google.com/site/anshulkundaje/projects/idr]. For peaks identified with the MACS2+DiffBind method, DiffBind [] was used to determine the differentially bound peaks from the sets of peaks called by MACS2 in at least 2 samples from all of the conditions tested. False discovery rate a […]

library_books

Histone H4 acetylation regulates behavioral inter individual variability in zebrafish

2018
Genome Biol
PMCID: 5922312
PMID: 29695303
DOI: 10.1186/s13059-018-1428-y

[…] were 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 bindi […]

library_books

DNA methylation profiles correlated to striped bass sperm fertility

2018
BMC Genomics
PMCID: 5894188
PMID: 29636007
DOI: 10.1186/s12864-018-4548-6

[…] le. 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 of the […]

library_books

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells

2018
PLoS One
PMCID: 5873942
PMID: 29590119
DOI: 10.1371/journal.pone.0193126

[…] notation of NF90/NF110 ChIP-seq peaks were computed using Hypergeometric Optimization of Motif EnRichment (HOMER) []. NF90/NF110 occupancy frequency in each chromatin state was computed in R with the DiffBind package []. […]

library_books

Atrx inactivation drives disease defining phenotypes in glioma cells of origin through global epigenomic remodeling

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

[…] rd.sourceforge.net). 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. […]

Citations

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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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