recipe bioconductor-cagefightr

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Homepage

https://bioconductor.org/packages/3.12/bioc/html/CAGEfightR.html

License

GPL-3 + file LICENSE

Recipe

/bioconductor-cagefightr/meta.yaml

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

package bioconductor-cagefightr

Versions

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

Depends

• bioconductor-biocgenerics >=0.36.0,<0.37.0

• bioconductor-biocparallel >=1.24.0,<1.25.0

• bioconductor-genomeinfodb >=1.26.0,<1.27.0

• bioconductor-genomicalignments >=1.26.0,<1.27.0

• bioconductor-genomicfeatures >=1.42.0,<1.43.0

• bioconductor-genomicfiles >=1.26.0,<1.27.0

• bioconductor-genomicinteractions >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-gviz >=1.34.0,<1.35.0

• bioconductor-interactionset >=1.18.0,<1.19.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-rtracklayer >=1.50.0,<1.51.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• r-assertthat >=0.2.0

• r-base >=4.0,<4.1.0a0

• r-matrix >=1.2-12

• r-pryr >=0.1.3

Required By

Installation

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

conda install bioconductor-cagefightr

and update with:

conda update bioconductor-cagefightr

or use the docker container:

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

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