- recipe bioconductor-rcas
RNA Centric Annotation System
- Homepage:
- License:
Artistic-2.0
- Recipe:
- 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-dt
>=0.2
r-knitr
>=1.12.3
r-plotly
>=4.5.2
r-rmarkdown
>=0.9.5
- 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:
[](http://bioconda.github.io/recipes/bioconductor-rcas/README.html)