recipe bioconductor-strandcheckr

Calculate strandness information of a bam file

Homepage:

https://bioconductor.org/packages/3.14/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:

1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

Depends:

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicalignments >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.14.0,<3.15.0

• r-base >=4.1,<4.2.0a0

• r-dplyr

• r-ggplot2

• r-gridextra

• r-magrittr

• r-reshape2

• r-rmarkdown

• r-stringr

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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