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RCAS

RNA Centric Annotation System


Bioconductor version: Release (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")):

Installation

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


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

BiocManager::install("RCAS")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RCAS")
How to do meta-analysis of multiple samples HTML R Script
Introduction - single sample analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, MotifAnnotation, MotifDiscovery, Software, Transcriptomics
Version 1.28.3
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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, seqLogo, utils, ranger, gprofiler2
System Requirements pandoc (>= 1.12.3)
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Suggests testthat, covr, BiocManager
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Depends On Me
Imports Me GenomicPlot
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Build Report Build Report

Package Archives

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

Source Package RCAS_1.28.3.tar.gz
Windows Binary RCAS_1.28.3.zip (64-bit only)
macOS Binary (x86_64) RCAS_1.28.3.tgz
macOS Binary (arm64) RCAS_1.28.3.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
Old Source Packages for BioC 3.18 Source Archive