recipe bioconductor-cager

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Homepage

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

License

GPL-3

Recipe

/bioconductor-cager/meta.yaml

Links

biotools: cager

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

package bioconductor-cager

Versions

1.30.0-0, 1.28.0-0, 1.26.0-1, 1.24.0-0, 1.22.3-0, 1.20.0-0, 1.18.1-0, 1.16.0-0

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-delayedarray >=0.14.0,<0.15.0

• 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-multiassayexperiment >=1.14.0,<1.15.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• 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)