RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
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.
Bioinformatics Platform.
Bora
B
Uyar
Bioinformatics Platform.
Dilmurat
D
Yusuf
Bioinformatics Platform.
Ricardo
R
Wurmus
Systems Biology of Gene Regulatory Elements.
Nikolaus
N
Rajewsky
Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, 13092 Berlin, Germany.
Uwe
U
Ohler
Bioinformatics Platform.
Altuna
A
Akalin
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002645:Chickens / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D016678:Genome; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome; D014584:User-Computer Interface
D012333:RNA, Messenger; D016601:RNA-Binding Proteins