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This map represents all the scientific publications referring to CSAR per scientific context
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CSAR specifications

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Unique identifier OMICS_00435
Name CSAR
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 1.32.0
Stability Stable
Requirements
stats, IRanges, GenomicRanges, utils, R(>=2.15.0), S4Vectors, GenomeInfoDb, ShortRead, Biostrings
Maintained Yes

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Publication for ChIP-Seq Analysis in R

CSAR citations

 (7)
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Evolution of DNA Binding Sites of a Floral Master Regulatory Transcription Factor

2015
Mol Biol Evol
PMCID: 4693976
PMID: 26429922
DOI: 10.1093/molbev/msv210

[…] ned. Sequence reads mapping to the plastid and mitochondrial genomes were eliminated. For A lyrata, only reads mapping to the 9 longest scaffolds were retained (scaffold length > 1 Mb). The R package CSAR was used for peak calling for each biological replicate independently with default parameter values except for backg, which was set to 5 for all the analyses except AlySEP3 ChIP-seq replicate 1 w […]

library_books

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

2015
Genome Biol
PMCID: 4378019
PMID: 25853185
DOI: 10.1186/s13059-015-0597-1

[…] e Bioconductor package NarrowPeaks []. Only MACS peaks also detected by NarrowPeaks were considered for further processing. Final sets of peaks were annotated to TAIR10 using the Bioconductor package CSAR []. Analysis of peak distribution over exon, intron, enhancer, proximal promoter, 5’ UTR and 3’ UTR was done in R using ChIPpeakAnno []. Proximal promoter and immediate downstream were considered […]

library_books

Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl

2014
eLife
PMCID: 4075450
PMID: 24867218
DOI: 10.7554/eLife.03031.025

[…] es was carried out on an Illumina HiSeq 2000. Sequences in Solexa FASTQ format were mapped to the Arabidopsis genome, TAIR9, using SOAP2. ARF6 binding peaks were identified using ChIP-Seq analysis R (CSAR) software with parameters (backg = 10, norm = −1, test = 'Ratio', times = 1e6, digits = 2) (). Binding peaks with FDR < 0.01 were defined as the ARF6 binding peak and used in further analyses. Ge […]

library_books

Genome wide data (ChIP seq) enabled identification of cell wall related and aquaporin genes as targets of tomato ASR1, a drought stress responsive transcription factor

2014
BMC Plant Biol
PMCID: 3923394
PMID: 24423251
DOI: 10.1186/1471-2229-14-29

[…] pret our high throughput DNA sequencing results. Our ChIP-seq data showed 225 peaks with different values of statistical significance. The results of ChIP-seq were also analyzed with Cisgenome [] and CSAR [], but these results gave false peaks and were thus discarded. Artifacts can arise because the annotated sequence of the tomato genome [] is not error-free, particularly regarding the copy numbe […]

library_books

Structural determinants of DNA recognition by plant MADS domain transcription factors

2013
Nucleic Acids Res
PMCID: 3936718
PMID: 24275492
DOI: 10.1093/nar/gkt1172

[…] e reads were mapped to the Arabidopsis thaliana (TAIR9) genome using SOAPv2 (). Reads mapped to multiple regions or to the mitochondria or chloroplast genome were discarded. We modified the R package CSAR () to generate read-enrichment score values at each single-nucleotide position, without performing peak calling. This score represents the ratio between density of reads overlapping a given nucle […]

library_books

Practical Guidelines for the Comprehensive Analysis of ChIP seq Data

2013
PLoS Comput Biol
PMCID: 3828144
PMID: 24244136
DOI: 10.1371/journal.pcbi.1003326

[…] equence such as GC content or mappability (BEADS ). Peaks are finally called above a user-defined SNR level. Models used for the statistical assessment of enriched regions (peaks) range from Poisson (CSAR ), local Poisson (MACS), negative binomial (CisGenome ) to zero-inflated negative binomial (ZINBA ), or even extend to more sophisticated machine learning modeling techniques such as Hidden Marko […]


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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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