QuasR aims to cover the whole analysis workflow of typical ultra-high throughput
sequencing experiments, starting from the raw sequence reads, over pre-processing and
alignment, up to quantification. A single R script can contain all steps of a complete
analysis, making it simple to document, reproduce or share the workflow containing all
relevant details.
The QuasR package integrates the functionality of several R packages
(such as IRanges and Rsamtools) and external software (e.g. bowtie,
through the Rbowtie package).
The package was originally created for in house use at the Friedrich Miescher Institute. Current contributors include:
- Michael Stadler
- Dimos Gaidatzis
- Charlotte Soneson
- Anita Lerch
- Florian Hahne
The current QuasR release supports the analysis of single read and
paired-end ChIP-seq (chromatin immuno-precipitation combined with sequencing), RNA-seq
(gene expression profiling by sequencing of RNA) and Bis-seq (measurement of DNA
methylation by sequencing of bisulfite-converted genomic DNA) experiments. Allele
specific alignment and quantification is also supported in all of these experiment
types. QuasR has been successfully used with data from Illumina, 454 Life Technologies
and SOLiD sequencers, the latter by using bam files created externally QuasR.
QuasR has been described in:
"QuasR: Quantify and Annotate Short Reads in R"
Gaidatzis, D. and Lerch, A. and Hahne, F. and Stadler, M.B.
Bioinformatics 2015, 31(7):1130-1132.
PubMed: 25417205, doi: 10.1093/bioinformatics/btu781
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