CSAR specifications


Unique identifier OMICS_00435
Alternative name ChIP-Seq Analysis in R
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data For each DNA mapped read: chromosome, location (bp), strand (+/-), read length (bp), and number of times mapped on the genome.
Input format Plain text, tabular data format
Output data Tables of genomic coordinates of significantly enriched region locations, level of enrichment per nucleotide position and the distance of enriched regions to annotated genomic features
Output format Tabular data format
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.26.0
Stability Stable
Requirements S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
Maintained Yes



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Publication for ChIP-Seq Analysis in R

CSAR institution(s)
Applied Bioinformatics, Plant Research International, Wageningen, Netherlands; Netherlands Bioinformatics Centre, Wageningen, Netherlands; Laboratory of Molecular Biology, Wageningen University, Wageningen, Netherlands; Bioscience, Plant Research International, Wageningen, Netherlands; Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
CSAR funding source(s)
This project was supported by grants from the Netherlands Bioinformatics Centre (NBIC), which is part of the Netherlands Genomics Initiative, and from the Netherlands Organization for Scientific Research (NWO; Horizon grant #93519020).

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