csaw statistics

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csaw specifications

Information


Unique identifier OMICS_10689
Name csaw
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of sorted and indexed files where each file contains aligned reads for one ChIP-seq sample.
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.14.1
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, IRanges, GenomicRanges, Rsamtools, S4Vectors, GenomeInfoDb, R(>=3.5), SummarizedExperiment, edgeR, Rcpp, BiocParallel, GenomicFeatures, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, Rhtslib
Maintained Yes

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Maintainers


  • person_outline Gordon Smyth <>
  • person_outline Aaron Lun <>

Publication for csaw

csaw in publications

 (3)
PMCID: 5836825
PMID: 29504911
DOI: 10.1186/s12864-018-4479-2

[…] of broad h3k4me3 peaks located in promoter regions (±1kb around tss of annotated genes) and required to have a peak-calling q-value ≤0.01., for differential enrichment (de) analysis, deseq2 [] and csaw [] r packages were used. in deseq2 workflow, reads with mapping quality (mapq) of at least 10 were counted at the predicted peak regions. peaks overlapping the dac blacklisted regions (encode […]

PMCID: 5763571
PMID: 29321036
DOI: 10.1186/s12989-017-0239-8

[…] of subpeaks present within the forward and reverse strands of the h3k4me3 and h3k27me3 immunoprecipitations, the average fragment length was determined for each event using the r package csaw []. the cross-correlation graph measures the delay distance, or number of base pairs, which separate distinctive subpeaks, also evaluating the consistency of fragment lengths within the data set […]

PMCID: 5944832
PMID: 29038090
DOI: 10.1289/EHP1937

[…] windows (peaks smaller than 300bp were expanded to 300 bp) within peaks was computed for each sample (323,243 windows). differential chromatin accessibility was detected using the r package csaw v. 1.2.1 (), which uses methods from the edger package (). normalization factors were computed to correct for compositional bias between samples with the windowcounts function (with […]


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csaw institution(s)
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
csaw funding source(s)
Supported by The University of Melbourne (Elizabeth and Vernon Puzey scholarship); National Health and Medical Research Council Program Grant [1054618]; National Health and Medical Research Council Fellowship [1058892]; Victorian State Government Operational Infrastructure Support; and the Australian Government NHMRC IRIIS.

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