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ChIP-Seq Analysis in R CSAR

An R package for the statistical analysis of ChIP-seq experiments. CSAR calculates single-nucleotide read-enrichment values, taking the average size of DNA fragments subjected to sequencing into account. After normalization, sample and control are compared using a test based on the ratio test or the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutations. Computational efficiency is achieved by implementing the most time-consuming functions in C++ and integrating these in the R package.

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CSAR classification

CSAR specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
Plain text, tabular data format
Output format:
Tabular data format
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
For each DNA mapped read: chromosome, location (bp), strand (+/-), read length (bp), and number of times mapped on the genome.
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
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
1.26.0
Requirements:
S4Vectors, IRanges, GenomeInfoDb, GenomicRanges

CSAR distribution

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CSAR support

Documentation

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Publications

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

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).

Link to literature

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