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Contents of README:The pyCRAC package is a collection of python scripts to analyse high throughput data generated by RNA-sequencing, especially of molecules crosslinked by UV to an immunoprecipitated protein of interest (i.e. data generated by CLIP or CRAC protocols). It can be used to remove duplicate reads,tackles directional libraries and reports sense and anti-sense hits. A pipeline that streamlines the analysis of a group of CRAC datasets is available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines and depends on the python package 'ruffus', also at slackbuilds.org. References Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8. PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. Webb S, Hector RD, Kudla G, Granneman S. Nature Communications, 2017; DOI: 10.1038/s41467-017-00025-5 Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress. van Nues R, Schweikert G, de Leau E, Selega A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G, Granneman S. If you want to run the test suite after installation, see README.tests. |
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Parent Directory - README 15-Apr-2023 02:19 1.2K README.tests 11-Mar-2022 06:34 339 pyCRAC.SlackBuild 15-Apr-2023 02:19 3.2K pyCRAC.info 22-Dec-2023 02:04 361 setup_slack.py 15-Apr-2023 02:19 3.2K slack-desc 14-Jun-2018 16:00 961 test_slack.sh 13-Apr-2019 02:03 9.7K
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