diff options
Diffstat (limited to 'academic/pyCRAC/README')
| -rw-r--r-- | academic/pyCRAC/README | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README new file mode 100644 index 0000000000..dd847d0935 --- /dev/null +++ b/academic/pyCRAC/README @@ -0,0 +1,27 @@ +The pyCRAC package is a collection of python2-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. + +Included is the pipeline used for the analysis of a group of CRAC data +sets. + +An R-function used for kinetic CRAC analysis can be found in +/usr/share/pyCRAC/kinetic_crac_pipeline + +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. |