# RCAS project [](https://travis-ci.org/BIMSBbioinfo/RCAS)  ## 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](http://bioconductor.org/packages/3.4/bioc/html/RCAS.html) `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](http://bioconductor.org/packages/release/bioc/vignettes/RCAS/inst/doc/RCAS.vignette.html) - [package vignette for multi-sample analysis](http://bioconductor.org/packages/release/bioc/vignettes/RCAS/inst/doc/RCAS.metaAnalysis.vignette.html) - [reference manual](http://bioconductor.org/packages/3.4/bioc/manuals/RCAS/man/RCAS.pdf) 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](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.4.2/RCAS.html) comparing the peak regions discovered via CLIP-sequencing experiments of the [RNA-binding protein FUS](http://www.uniprot.org/uniprot/P35637) by [Nakaya et al, 2013](https://www.ncbi.nlm.nih.gov/pubmed/23389473), [Synaptic Functional Regulator FMR1](http://www.uniprot.org/uniprot/Q06787) by [Ascano et al. 2012](https://www.ncbi.nlm.nih.gov/pubmed/23235829), and [Eukaryotic initiation factor 4A-III](http://www.uniprot.org/uniprot/P38919) by [Sauliere et al, 2012](https://www.ncbi.nlm.nih.gov/pubmed/23085716). ### Single Sample Analysis Use Cases - [RCAS report](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.1.1/PARCLIP_PUM2_Hafner2010b_hg19.bed.RCAS.report.html) for [PUM2](http://www.uniprot.org/uniprot/Q8TB72) RNA-binding sites detected by **PAR-CLIP** technique ([Hafner et al, 2010](https://www.ncbi.nlm.nih.gov/pubmed/20371350)) - input: [PARCLIP_PUM2_Hafner2010b_hg19](http://dorina.mdc-berlin.de/api/v1.0/download/regulator/hg19/PARCLIP_PUM2_Hafner2010b_hg19) - [RCAS report](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.1.1/PARCLIP_QKI_Hafner2010c_hg19.bed.RCAS.report.html) for [QKI](http://www.uniprot.org/uniprot/Q96PU8) RNA-binding sites detected by **PAR-CLIP** technique ([Hafner et al, 2010](https://www.ncbi.nlm.nih.gov/pubmed/20371350)) - input: [PARCLIP_QKI_Hafner2010c_hg19](http://dorina.mdc-berlin.de/api/v1.0/download/regulator/hg19/PARCLIP_QKI_Hafner2010c_hg19 ) - [RCAS report](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.1.1/PARCLIP_IGF2BP123_Hafner2010d_hg19.bed.RCAS.report.html) for IGF2BP[1](http://www.uniprot.org/uniprot/Q9NZI8)[2](http://www.uniprot.org/uniprot/Q9Y6M1)[3](http://www.uniprot.org/uniprot/O00425) RNA-binding sites detected by **PAR-CLIP** technique ([Hafner et al, 2010](https://www.ncbi.nlm.nih.gov/pubmed/20371350)) - input: [PARCLIP_IGF2BP123_Hafner2010d_hg19](http://dorina.mdc-berlin.de/api/v1.0/download/regulator/hg19/PARCLIP_IGF2BP123_Hafner2010d_hg19) - [RCAS report](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.1.1/human_FANTOM4_tiRNAs-hg19.bed.RCAS.report.html) for tiny RNA (tiRNA) loci detected by **deepCAGE** analysis ([Taft et al. 2009](https://www.ncbi.nlm.nih.gov/pubmed/19377478)) - input: [human_FANTOM4_tiRNAs.bed](http://fantom.gsc.riken.jp/4/download/Supplemental_Materials/Taft_et_al_2009/human_FANTOM4_tiRNAs.bed) - [RCAS report](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.1.1/m1Asites.dominissini.2016.resized.bed.RCAS.report.html) for m¹A **methylation sites** ([Dominissini et al, 2016](https://www.ncbi.nlm.nih.gov/pubmed/26863196)) - input: [GSE70485_human_peaks.txt.gz](http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE70485&format=file&file=GSE70485%5Fhuman%5Fpeaks%2Etxt%2Egz) ## 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](https://academic.oup.com/nar/article/3038237/RCAS-an-RNA-centric-annotation-system-for). ## Acknowledgements RCAS is developed in the group of [Altuna Akalin](http://bioinformatics.mdc-berlin.de/team.html#altuna-akalin-phd) (head of the Scientific Bioinformatics Platform) by [Bora Uyar](http://bioinformatics.mdc-berlin.de/team.html#bora-uyar-phd) (Bioinformatics Scientist), [Dilmurat Yusuf](http://bioinformatics.mdc-berlin.de/team.html#dilmurat-yusuf-phd) (Bioinformatics Scientist) and [Ricardo Wurmus](http://bioinformatics.mdc-berlin.de/team.html#ricardo-wurmus) (System Administrator) at the Berlin Institute of Medical Systems Biology ([BIMSB](https://www.mdc-berlin.de/13800178/en/bimsb)) at the Max-Delbrueck-Center for Molecular Medicine ([MDC](https://www.mdc-berlin.de)) in Berlin. RCAS is developed as a bioinformatics service as part of the [RNA Bioinformatics Center](http://www.denbi.de/index.php/rbc), which is one of the eight centers of the German Network for Bioinformatics Infrastructure ([de.NBI](http://www.denbi.de/)).