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>
citation("RCAS")):
Installation
To install this package, start R (version "4.0") 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 | 1.14.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 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 |
| System Requirements | pandoc (>= 1.12.3) |
| URL |
See More
| Suggests | testthat, covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.14.0.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 |
| 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 3.11 | Source Archive |