RCAS
This is the released version of RCAS; for the devel version, see RCAS.
RNA Centric Annotation System
Bioconductor version: Release (3.23)
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")):Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Altuna Akalin. RCAS: RNA Centric Annotation System. doi:10.18129/B9.bioc.RCAS, R package version 1.38.0, https://bioconductor.org/packages/RCAS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RCAS_1.38.0.tar.gz |
| Windows Binary (x86_64) | RCAS_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | RCAS_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | RCAS_1.38.0.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 |