DOI: 10.18129/B9.bioc.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 (from within R, enter citation("RCAS")):


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HTML R Script How to do meta-analysis of multiple samples
HTML R Script Introduction - single sample analysis
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biocViews Coverage, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, MotifAnnotation, MotifDiscovery, Software, Transcriptomics
Version 1.14.0
In Bioconductor since BioC 3.4 (R-3.3) (4 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
Suggests testthat, covr
SystemRequirements pandoc (>= 1.12.3)
Depends On Me
Imports Me
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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
Package Short Url https://bioconductor.org/packages/RCAS/
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