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Open Source Science

https://github.com/bioconductor-source/quasr

https://github.com/bioconductor-source/quasr

Science Score: 49.0%

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    CITATION.cff file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
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Last synced: 6 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 2.33 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed 10 months ago
Metadata Files
Readme

README.md


Quantify and annotate short reads in R


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:

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, doi: 10.1093/bioinformatics/btu781

Download from Bioconductor

QuasR download page

Software status

| Platforms | OS | R CMD check | Coverage | |:------------------:|:----------------:|:----------------:|:----------------:| | Github-Actions | Multiple | R build status | Codecov.io coverage status | | Bioc (devel) | Multiple | Bioconductor-devel Build Status | Codecov.io coverage status | | Bioc (release) | Multiple | Bioconductor-release Build Status | Codecov.io coverage status |

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

GitHub Events

Total
  • Member event: 1
  • Push event: 5
  • Create event: 1
Last Year
  • Member event: 1
  • Push event: 5
  • Create event: 1

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • actions/upload-artifact v3 composite
  • grimbough/bioc-actions/build-install-check v1 composite
  • grimbough/bioc-actions/run-BiocCheck v1 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/run_rchk.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/run-rchk master composite
DESCRIPTION cran
  • GenomicRanges * depends
  • R >= 4.4 depends
  • Rbowtie * depends
  • parallel * depends
  • AnnotationDbi * imports
  • BSgenome * imports
  • Biobase * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • GenomicFeatures * imports
  • GenomicFiles * imports
  • IRanges * imports
  • Rsamtools >= 2.13.1 imports
  • S4Vectors * imports
  • ShortRead * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • rtracklayer * imports
  • stats * imports
  • tools * imports
  • txdbmaker * imports
  • utils * imports
  • BiocStyle * suggests
  • GenomicAlignments * suggests
  • Gviz * suggests
  • Rhisat2 * suggests
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
inst/AlignerIndexPkg-template/DESCRIPTION cran
  • GENOMENAME * depends