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]|
|Bioconductor views||Coverage GO GeneSetEnrichment GeneTarget GenomeAnnotation MotifAnnotation MotifDiscovery Software Transcriptomics|
|Maintainer||Bora Uyar <firstname.lastname@example.org>|
|Package repository||View on Bioconductor|
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