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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/RCAS/ |
| Package Short Url | https://bioconductor.org/packages/RCAS/ |
| Package Downloads Report | Download Stats |