recipe bioconductor-strandcheckr

Calculate strandness information of a bam file

Homepage

https://bioconductor.org/packages/3.11/bioc/html/strandCheckR.html

License

GPL (>= 2)

Recipe

/bioconductor-strandcheckr/meta.yaml

This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.

package bioconductor-strandcheckr

Versions

1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicalignments >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.10.0,<3.11.0

• r-base >=4.0,<4.1.0a0

• r-dplyr

• r-ggplot2

• r-gridextra

• r-magrittr

• r-reshape2

• r-stringr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-strandcheckr

and update with:

conda update bioconductor-strandcheckr

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-strandcheckr:<tag>

(see bioconductor-strandcheckr/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-strandcheckr/README.html)