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QuasR: quantification and annotation of short reads in R.

ABSTRACT: QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.QuasR is implemented in R and C/C++. Source code and binaries for major platforms (Linux, OS X and MS Windows) are available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/QuasR.html). The package includes a 'vignette' with step-by-step examples for typical work ?ows.Supplementary data are available at Bioinformatics online.

SUBMITTER: Gaidatzis D

PROVIDER: S-EPMC4382904 | biostudies-other | 2015 Apr

REPOSITORIES: biostudies-other

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QuasR: quantification and annotation of short reads in R.

Gaidatzis Dimos D Lerch Anita A Hahne Florian F Stadler Michael B MB

Bioinformatics (Oxford, England) 20141121 7

<h4>Unlabelled</h4>QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.<h4>Availabili ...[more]

PMID: 25417205

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