recipe bioconductor-cager

Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

Homepage

https://bioconductor.org/packages/3.8/bioc/html/CAGEr.html

License

GPL-3

Recipe

/bioconductor-cager/meta.yaml

Links

biotools: cager

package bioconductor-cager

Versions

1.24.0-0, 1.22.3-0, 1.20.0-0, 1.18.1-0, 1.16.0-0

Depends

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biocparallel >=1.16.0,<1.17.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-delayedarray >=0.8.0,<0.9.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicalignments >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-multiassayexperiment >=1.8.0,<1.9.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• r-base >=3.5.1,<3.5.2.0a0

• r-beanplot

• r-data.table

• r-formula.tools

• r-ggplot2 >=2.2.0

• r-gtools

• r-kernsmooth

• r-memoise

• r-plyr

• r-reshape

• r-som

• r-stringdist

• r-stringi

• r-vegan

• r-vgam

Required By

Installation

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

conda install bioconductor-cager

and update with:

conda update bioconductor-cager

or use the docker container:

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

(see bioconductor-cager/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-cager/README.html)