RCAS

DOI: 10.18129/B9.bioc.RCAS    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see RCAS.

RNA Centric Annotation System

Bioconductor version: 3.11

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 "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Coverage, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, MotifAnnotation, MotifDiscovery, Software, Transcriptomics
Version	1.14.0
In Bioconductor since	BioC 3.4 (R-3.3) (4 years)
License	Artistic-2.0
Depends	R (>= 3.3.0), 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)
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RCAS_1.14.0.tar.gz
Windows Binary	RCAS_1.14.0.zip
macOS 10.13 (High Sierra)	RCAS_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RCAS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RCAS
Package Short Url	https://bioconductor.org/packages/RCAS/
Package Downloads Report	Download Stats