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/3.14/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:

2.0.1-0,  1.34.0-0,  1.32.1-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.24.0-0,  1.22.3-0, 

2.0.1-0,  1.34.0-0,  1.32.1-0,  1.32.0-0,  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 >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-delayedarray >=0.20.0,<0.21.0

• bioconductor-delayedmatrixstats >=1.16.0,<1.17.0

• 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-multiassayexperiment >=1.20.0,<1.21.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-data.table

• r-formula.tools

• r-ggplot2 >=2.2.0

• r-gtools

• r-kernsmooth

• r-memoise

• r-plyr

• r-reshape2

• r-som

• r-stringdist

• r-stringi

• r-vegan

• r-vgam

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

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)