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Riborex\n\nRiborex is a R package for identification of differential translation from Ribo-seq data.\n\n--------------------------------------------------------\n\n[Online Paper](https://academic.oup.com/bioinformatics/article/33/11/1735/2964727) | [PDF](https://watermark.silverchair.com/btx047.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAr0wggK5BgkqhkiG9w0BBwagggKqMIICpgIBADCCAp8GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMEeGzK92KGEWtk0FoAgEQgIICcFUmPpYJo1tGujsBoP4lYse6EnU5MCy_Hp5z2ae7rC9jSUgL4I_UscKpEadF2YIwltYzPiN63ZHToP6ec-l8MPEDHwrFISgfjFkYiz7CdWwTLFo-1zKx449YprMc7gPtXGUjF4koXDC0VUKEAz5Df6litXeErwErQfN1MvTfapzv6e2uocdeaIb_gVHP8_SOgzivRHJ5iFDunIjS_43s_G5N42L4lIOAaEl_5gKQ7MmBoH04Nzd8yc8GX9Q6D5gBri-Lqsu3HM5x4_EuGRrAp8dP40rtwCBF7yoPj_VHhirTgN1XP82JZJO7QWzqnsZXJ6n9w4lOTgxpY24DONTXGAVAAf-CwkuIK58cvqvrulZwOwj9cikYExj5sXpYY9J4u1y-wVufDIFBLa912qaVRJV9h7k3nGihq7MJkpNKLwTzqj35VbtmGDgqoDJMQxjs9K5WdSCW4Ecc6uPFQk9XwC7PzYAiJIRn7mjVUjyciBKe9XRvcpJbK4C3nl__XDRhM9sFmNlA7mwPhIePhOhzhLWACUSCltLBPiRNDNv34VB_Rj_--SPxG5gnRmfqGew7GeDYUo_W-rjvCC0PeBASozZUe3h6sT4s7eIXwWLbzuJ_ujWcXM7jLaqCjJgl-SGUcEYUiWUvXK9YfGNshpgAf99cCpu4mNhGxPL672URz1_RhY2kS2zHbG84MOgdd-SqvarTGYugArsUN6AlMXvHTR5ZIWr4PE47FjOYPCn4NS9QV-42dpj1a7TuJSsDlbDdoHdXcxXTTFhO_wfKjVy_OCXR1jrqxSHTURi3NR6yF0W4mO-oCuTM7DS4RtI1LvnhDA) | [Supplementary File](https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/33/11/10.1093_bioinformatics_btx047/3/btx047_supp.pdf?Expires=1620962473\u0026Signature=h3eYZdiu4ddVx5L-NXUsO123Ej50pLrumpFn74i1FjsaS7wbQNqrJqMZg4G9XKryOWUJXNBDLxeTnYBXOKPHW5O1QFuDS6k8r8gvjwSMpEtOMdR0wP1tsnhKKi~Oi8sBIPEdHalsQcJCZMZXkNuKpav7u~dgDZ2pUkhiaGoOyLomnBHfafjM79-Lprnk4NLFO3KzOOZ0-IPtSvVDYczqEo8HascrsO1B3Rbs-1aQdQv8~hoTAfV7Y8hXOA3XO2WSO1Kp16qrgmqUWCtqJUfd6QZPlwy~JbZ4OS9HPjTNyM4e0JVWLuWNsjN4~aQixjZ9S9JEzEmmnBHGndxaH6Xs~g__\u0026Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)\n\n--------------------------------------------------------\n\n## DEPENDENCIES\n* DESeq2\n* edgeR\n* fdrtool\n--------------------------------------------------------\n## INSTALLATION\nWe strongly recommend that you install Riborex via conda:\n```bash\n   conda install -c bioconda r-riborex\n```\nTo install locally, please make sure you have DESeq2 and edgeR installed.\nThen start R and enter:\n```r\n  ## try http:// if https:// URLs are not supported\n  source(\"https://bioconductor.org/biocLite.R\")\n  biocLite(\"DESeq2\")\n  biocLite(\"edgeR\")\n  biocLite('fdrtool')\n```\nTo install Riborex, download the latest version\n\"riborex-x.x.x.tar.gz\" from releases\nat https://github.com/smithlabcode/riborex, start\na terminal and CD into the directory where you downloaded Riborex,\nstart R and enter\n```r\n  install.packages(\"riborex-x.x.x.tar.gz\", repos=NULL, type=\"source\")\n```\nAlternatively, you could also install `devtools` package and then install\n`riborex` to get latest changes :\n\n```r\n  install.packages('devtools')\n  library(devtools)\n  options(unzip='internal')\n  devtools::install_github('smithlabcode/riborex')\n```\n--------------------------------------------------------\n\n## DOCUMENTATION\nPlease refer to vignettes/riborex.pdf for how to use riborex.\n\n## Contacts and bug reports\nAndrew D. Smith\nandrewds@usc.edu\n\nWenzheng Li\nwenzhenl@usc.edu\n\nWeili Wang\nweiliw@usc.edu\n\nIf you found a bug or mistake in this project, we would like to know about it.\nBefore you send us the bug report though, please check the following:\n\n1. Are you using the latest version? The bug you found may already have been\n   fixed.\n2. Check that your input is in the correct format and you have selected the\n   correct options.\n3. Please reduce your input to the smallest possible size that still produces\n   the bug; we will need your input data to reproduce the problem, and the\n   smaller you can make it, the easier it will be.\n\n--------------------------------------------------------\n## Copyright and License Information\nCopyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang\nand Andrew D. Smith\n\nAuthors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith\n\nThis program is free software: you can redistribute it and/or modify it under\nthe terms of the GNU General Public License as published by the Free Software\nFoundation, either version 3 of the License, or (at your option) any later\nversion.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT\nANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS\nFOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License along with\nthis program. If not, see http://www.gnu.org/licenses/.\n","funding_links":[],"categories":["Differential Analysis"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Friborex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2Friborex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Friborex/lists"}