<img src="vignettes/QuasR-logo.png" align="left" alt="" /> <br> # Quantify and annotate short reads in R <br> ## Overview `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](https://github.com/mbstadler) - Dimos Gaidatzis - [Charlotte Soneson](https://github.com/csoneson) - Anita Lerch - Florian Hahne ## Functionality 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`. ## Reference `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](https://www.ncbi.nlm.nih.gov/pubmed/25417205), [doi: 10.1093/bioinformatics/btu781](https://doi.org/10.1093/bioinformatics/btu781) ## Download from Bioconductor [QuasR download page](https://bioconductor.org/packages/QuasR/) ## Software status | Platforms | OS | R CMD check | Coverage | |:------------------:|:----------------:|:----------------:|:----------------:| | Github-Actions | Multiple | [](https://github.com/fmicompbio/QuasR/actions) | [](https://codecov.io/github/fmicompbio/QuasR) | | Bioc ([_devel_](http://bioconductor.org/packages/devel/bioc/html/QuasR.html)) | Multiple | [](http://bioconductor.org/checkResults/devel/bioc-LATEST/QuasR) | [](https://codecov.io/github/fmicompbio/QuasR) | | Bioc ([_release_](http://bioconductor.org/packages/release/bioc/html/QuasR.html)) | Multiple | [](http://bioconductor.org/checkResults/release/bioc-LATEST/QuasR) | [](https://codecov.io/github/fmicompbio/QuasR) |