{"id":13711887,"url":"https://github.com/BIMSBbioinfo/RCAS","last_synced_at":"2025-05-06T21:32:37.979Z","repository":{"id":78488610,"uuid":"43009681","full_name":"BIMSBbioinfo/RCAS","owner":"BIMSBbioinfo","description":"R package for the RNA Centric Annotation System (RCAS)","archived":false,"fork":false,"pushed_at":"2024-02-04T20:31:36.000Z","size":15325,"stargazers_count":6,"open_issues_count":4,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-11-13T22:35:09.862Z","etag":null,"topics":["bioconductor","cage","coverage-distribution","go","interactive-plots","modification","motif-discovery","msigdb","par-clip","protein-rna-interactions","reporting","rna"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BIMSBbioinfo.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-09-23T15:29:13.000Z","updated_at":"2024-06-10T16:05:50.000Z","dependencies_parsed_at":"2024-02-09T22:32:07.616Z","dependency_job_id":null,"html_url":"https://github.com/BIMSBbioinfo/RCAS","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2FRCAS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2FRCAS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2FRCAS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2FRCAS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BIMSBbioinfo","download_url":"https://codeload.github.com/BIMSBbioinfo/RCAS/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252772188,"owners_count":21801871,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","cage","coverage-distribution","go","interactive-plots","modification","motif-discovery","msigdb","par-clip","protein-rna-interactions","reporting","rna"],"created_at":"2024-08-02T23:01:12.637Z","updated_at":"2025-05-06T21:32:36.917Z","avatar_url":"https://github.com/BIMSBbioinfo.png","language":"R","readme":"# RCAS project\n\n[![Build Status](https://travis-ci.org/BIMSBbioinfo/RCAS.svg?branch=master)](https://travis-ci.org/BIMSBbioinfo/RCAS)\n![codecov.io](https://codecov.io/github/BIMSBbioinfo/RCAS/coverage.svg?branch=master)\n\n## Introduction\n\nRCAS is an R/Bioconductor package designed as a generic reporting tool for the\nfunctional analysis of transcriptome-wide regions of interest detected by\nhigh-throughput experiments. Such transcriptomic regions could be, for instance,\nsignal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites,\nRNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any\nother collection of query regions at the level of the transcriptome. RCAS\nproduces in-depth annotation summaries and coverage profiles based on the\ndistribution of the query regions with respect to transcript features (exons,\nintrons, 5’/3’ UTR regions, exon-intron boundaries, promoter regions). Moreover,\nRCAS can carry out functional enrichment analyses and discriminative motif\ndiscovery. RCAS supports all genome versions that are available in\n`BSgenome::available.genomes`\n\n## installation:\n\n### Installing from [Bioconductor](http://bioconductor.org/packages/3.4/bioc/html/RCAS.html)\n`if (!requireNamespace(\"BiocManager\", quietly=TRUE))`\n    `install.packages(\"BiocManager\")`\n\n`BiocManager::install('RCAS')`\n\n### Installing the development version from Github\n```\nlibrary('devtools')\ndevtools::install_github('BIMSBbioinfo/RCAS')\n```\n\n### Installing via Bioconda channel\n\n`conda install bioconductor-rcas -c bioconda`\n\n### Installing via Guix\n\n`guix package -i r r-rcas`\n\n## usage:\n\n### Package vignettes and reference manual\n\nFor detailed instructions on how to use RCAS, please see: \n  - [package vignette for single sample analysis](http://bioconductor.org/packages/release/bioc/vignettes/RCAS/inst/doc/RCAS.vignette.html) \n  - [package vignette for multi-sample analysis](http://bioconductor.org/packages/release/bioc/vignettes/RCAS/inst/doc/RCAS.metaAnalysis.vignette.html)\n  - [reference manual](http://bioconductor.org/packages/3.4/bioc/manuals/RCAS/man/RCAS.pdf) for more information about the detailed functions available in RCAS.\n\n## Use cases from published RNA-based omics datasets\n\n### Multi-sample analysis use case\n\n- 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).\n\n\n### Single Sample Analysis Use Cases\n\n- [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))\n  - input:  [PARCLIP_PUM2_Hafner2010b_hg19](http://dorina.mdc-berlin.de/api/v1.0/download/regulator/hg19/PARCLIP_PUM2_Hafner2010b_hg19)\n\n\n- [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))\n  - input: [PARCLIP_QKI_Hafner2010c_hg19](http://dorina.mdc-berlin.de/api/v1.0/download/regulator/hg19/PARCLIP_QKI_Hafner2010c_hg19 )\n\n\n- [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))\n  - input:  [PARCLIP_IGF2BP123_Hafner2010d_hg19](http://dorina.mdc-berlin.de/api/v1.0/download/regulator/hg19/PARCLIP_IGF2BP123_Hafner2010d_hg19)\n\n\n- [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))\n    - input: [human_FANTOM4_tiRNAs.bed](http://fantom.gsc.riken.jp/4/download/Supplemental_Materials/Taft_et_al_2009/human_FANTOM4_tiRNAs.bed)\n\n\n- [RCAS report](https://bimsbstatic.mdc-berlin.de/akalin/buyar/RCAS/1.1.1/m1Asites.dominissini.2016.resized.bed.RCAS.report.html) for m\u003csup\u003e1\u003c/sup\u003eA **methylation sites** ([Dominissini et al, 2016](https://www.ncbi.nlm.nih.gov/pubmed/26863196))\n    - input: [GSE70485_human_peaks.txt.gz](http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE70485\u0026format=file\u0026file=GSE70485%5Fhuman%5Fpeaks%2Etxt%2Egz)\n\n## Citation\nIn order to cite RCAS, please use: \n\nBora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin; RCAS: an RNA centric annotation\n  system for transcriptome-wide regions of interest. Nucleic Acids Res 2017 gkx120. doi: 10.1093/nar/gkx120\n\nSee our publication [here](https://academic.oup.com/nar/article/3038237/RCAS-an-RNA-centric-annotation-system-for). \n\n## Acknowledgements\n\nRCAS is developed in the group of\n[Altuna Akalin](http://bioinformatics.mdc-berlin.de/team.html#altuna-akalin-phd)\n(head of the Scientific Bioinformatics Platform) by\n[Bora Uyar](http://bioinformatics.mdc-berlin.de/team.html#bora-uyar-phd)\n(Bioinformatics Scientist),\n[Dilmurat Yusuf](http://bioinformatics.mdc-berlin.de/team.html#dilmurat-yusuf-phd)\n(Bioinformatics Scientist) and\n[Ricardo Wurmus](http://bioinformatics.mdc-berlin.de/team.html#ricardo-wurmus)\n(System Administrator) at the Berlin Institute of Medical Systems Biology\n([BIMSB](https://www.mdc-berlin.de/13800178/en/bimsb))\nat the Max-Delbrueck-Center for Molecular Medicine\n([MDC](https://www.mdc-berlin.de)) in Berlin.\n\nRCAS is developed as a bioinformatics service as part of\nthe [RNA Bioinformatics Center](http://www.denbi.de/index.php/rbc),\nwhich is one of the eight centers of\nthe German Network for Bioinformatics Infrastructure\n([de.NBI](http://www.denbi.de/)).\n","funding_links":[],"categories":["Repositories"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBIMSBbioinfo%2FRCAS","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FBIMSBbioinfo%2FRCAS","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBIMSBbioinfo%2FRCAS/lists"}