RCAS

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>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RCAS")

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

Documentation

PDF		Reference Manual

Details

biocViews	Coverage, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, MotifAnnotation, MotifDiscovery, Software, Transcriptomics
Version	1.27.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 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
LinkingTo
Suggests	testthat, covr
SystemRequirements	pandoc (>= 1.12.3)
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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)
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