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RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

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Item Type:Article
Title:RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
Creators Name:Uyar, B. and Yusuf, D. and Wurmus, R. and Rajewsky, N. and Ohler, U. and Akalin, A.
Abstract:In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de.
Keywords:Base Sequence, Binding Sites, Computational Biology, Genome, Messenger RNA, Molecular Sequence Annotation, Protein Binding, RNA-Binding Proteins, Transcriptome, User-Computer Interface, Animals, Chickens, Drosophila melanogaster
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press (U.K.)
Volume:45
Number:10
Page Range:e91
Date:2 June 2017
Official Publication:https://doi.org/10.1093/nar/gkx120
PubMed:View item in PubMed

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