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.