DOI: 10.18129/B9.bioc.RCAS  

This is the development version of RCAS; for the stable release version, see RCAS.

RNA Centric Annotation System

Bioconductor version: Development (3.18)

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.

Author: Bora Uyar [aut, cre], Dilmurat Yusuf [aut], Ricardo Wurmus [aut], Altuna Akalin [aut]

Maintainer: Bora Uyar <bora.uyar at mdc-berlin.de>

Citation (from within R, enter citation("RCAS")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


PDF   Reference Manual


biocViews Coverage, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, MotifAnnotation, MotifDiscovery, Software, Transcriptomics
Version 1.27.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License Artistic-2.0
Depends R (>= 3.5.0), plotly (>= 4.5.2), DT (>= 0.2), data.table
Imports GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb(>= 1.12.0), Biostrings, rtracklayer, GenomicFeatures, rmarkdown (>= 0.9.5), genomation(>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot, ggseqlogo, utils, ranger, gprofiler2
Suggests testthat, covr
SystemRequirements pandoc (>= 1.12.3)
Depends On Me
Imports Me GenomicPlot
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary RCAS_1.27.0.zip
macOS Binary (x86_64) RCAS_1.27.0.tgz
macOS Binary (arm64) RCAS_1.27.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RCAS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RCAS
Bioc Package Browser https://code.bioconductor.org/browse/RCAS/
Package Short Url https://bioconductor.org/packages/RCAS/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: