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/3.9/bioc/html/CAGEr.html

License

GPL-3

Recipe

/bioconductor-cager/meta.yaml

Links

biotools: cager

package bioconductor-cager

(downloads) docker_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

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-bsgenome

>=1.50.0,<1.51.0

Depends bioconductor-delayedarray

>=0.8.0,<0.9.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-multiassayexperiment

>=1.8.0,<1.9.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-beanplot

Depends r-data.table

Depends r-formula.tools

Depends r-ggplot2

>=2.2.0

Depends r-gtools

Depends r-kernsmooth

Depends r-memoise

Depends r-plyr

Depends r-reshape

Depends r-som

Depends r-stringdist

Depends r-stringi

Depends r-vegan

Depends r-vgam

Requirements

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>)