recipe bioconductor-rcas

RNA Centric Annotation System

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/RCAS.html

License:

Artistic-2.0

Recipe:

/bioconductor-rcas/meta.yaml

Links:

biotools: rcas

RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery.

package bioconductor-rcas

Versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.1-0,  1.8.0-0, 

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.1-0,  1.8.0-0,  1.6.0-0,  1.5.4-2,  1.5.4-0,  1.4.0-0,  1.2.0-0,  1.1.1-0,  1.0.0-0,  1.0.0.dev75225b9-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0

• bioconductor-genomation >=1.30.0,<1.31.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• pandoc >=1.12.3

• r-base >=4.2,<4.3.0a0

• r-cowplot

• r-data.table

• r-dt >=0.2

• r-ggplot2

• r-ggseqlogo

• r-gprofiler2

• r-knitr >=1.12.3

• r-pbapply

• r-pheatmap

• r-plotly >=4.5.2

• r-plotrix

• r-proxy

• r-ranger

• r-rmarkdown >=0.9.5

• r-rsqlite

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-rcas

and update with:

conda update bioconductor-rcas

or use the docker container:

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

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