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QuasR: quantification and annotation of short reads in R
Open accessAbstract
Summary: 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. Availability and implementation: 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 flows. Contact: michael.stadler@fmi.ch Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
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Metadata
- Authors
- Gaidatzis, D., Lerch, A., Hahne, F., & Stadler, M. B.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-12-09
- Volume
- 31
- Issue
- 7
- Pages
- 1130-1132
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2143215863
- Cited by
- 314
- References
- 1
- FWCI
- 5.96
- Type
- journal article
- Language
- en
- Open access
- hybrid
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