RCAS
This is thereleased version of RCAS; for the devel version, seeRCAS.
RNA Centric Annotation System
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("RCAS")For older versions of R, please refer to the appropriateBioconductor 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 | 1.36.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 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
FollowInstallation instructions to use this package in your R session.
| Source Package | RCAS_1.36.0.tar.gz |
| Windows Binary (x86_64) | RCAS_1.36.0.zip (64-bit only) |
| macOS Binary (x86_64) | RCAS_1.36.0.tgz |
| macOS Binary (arm64) | RCAS_1.36.0.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 |