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# RCAS project [![Build Status](]( ![]( ## Introduction 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. RCAS supports all genome versions that are available in `BSgenome::available.genomes` ## installation: ### Installing from [Bioconductor]( `if (!requireNamespace("BiocManager", quietly=TRUE))` `install.packages("BiocManager")` `BiocManager::install('RCAS')` ### Installing the development version from Github ``` library('devtools') devtools::install_github('BIMSBbioinfo/RCAS') ``` ### Installing via Bioconda channel `conda install bioconductor-rcas -c bioconda` ### Installing via Guix `guix package -i r r-rcas` ## usage: ### Package vignettes and reference manual For detailed instructions on how to use RCAS, please see: - [package vignette for single sample analysis]( - [package vignette for multi-sample analysis]( - [reference manual]( for more information about the detailed functions available in RCAS. ## Use cases from published RNA-based omics datasets ### Multi-sample analysis use case - See an [example report]( comparing the peak regions discovered via CLIP-sequencing experiments of the [RNA-binding protein FUS]( by [Nakaya et al, 2013](, [Synaptic Functional Regulator FMR1]( by [Ascano et al. 2012](, and [Eukaryotic initiation factor 4A-III]( by [Sauliere et al, 2012]( ### Single Sample Analysis Use Cases - [RCAS report]( for [PUM2]( RNA-binding sites detected by **PAR-CLIP** technique ([Hafner et al, 2010]( - input: [PARCLIP_PUM2_Hafner2010b_hg19]( - [RCAS report]( for [QKI]( RNA-binding sites detected by **PAR-CLIP** technique ([Hafner et al, 2010]( - input: [PARCLIP_QKI_Hafner2010c_hg19]( ) - [RCAS report]( for IGF2BP[1]([2]([3]( RNA-binding sites detected by **PAR-CLIP** technique ([Hafner et al, 2010]( - input: [PARCLIP_IGF2BP123_Hafner2010d_hg19]( - [RCAS report]( for tiny RNA (tiRNA) loci detected by **deepCAGE** analysis ([Taft et al. 2009]( - input: [human_FANTOM4_tiRNAs.bed]( - [RCAS report]( for m<sup>1</sup>A **methylation sites** ([Dominissini et al, 2016]( - input: [GSE70485_human_peaks.txt.gz]( ## Citation In order to cite RCAS, please use: Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin; RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. Nucleic Acids Res 2017 gkx120. doi: 10.1093/nar/gkx120 See our publication [here]( ## Acknowledgements RCAS is developed in the group of [Altuna Akalin]( (head of the Scientific Bioinformatics Platform) by [Bora Uyar]( (Bioinformatics Scientist), [Dilmurat Yusuf]( (Bioinformatics Scientist) and [Ricardo Wurmus]( (System Administrator) at the Berlin Institute of Medical Systems Biology ([BIMSB]( at the Max-Delbrueck-Center for Molecular Medicine ([MDC]( in Berlin. RCAS is developed as a bioinformatics service as part of the [RNA Bioinformatics Center](, which is one of the eight centers of the German Network for Bioinformatics Infrastructure ([de.NBI](