RCAS
RNA Centric Annotation System
Bioconductor version: Release (3.19)
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("RCAS")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | Coverage, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, MotifAnnotation, MotifDiscovery, Software, Transcriptomics |
Version | 1.30.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (8 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, txdbmaker, 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) |
URL |
See More
Suggests | testthat, covr, BiocManager |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | GenomicPlot |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | RCAS_1.30.0.tar.gz |
Windows Binary | RCAS_1.30.0.zip (64-bit only) |
macOS Binary (x86_64) | RCAS_1.30.0.tgz |
macOS Binary (arm64) | RCAS_1.30.0.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 |