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14.2 > Academic > pyCRAC (1.2.4.0)

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.

This requires: pandas, numpy, scipy, ruffus, flexbar, pysam, novocraft

Maintained by: rob van nues
Keywords: python,sequence alignment
ChangeLog: pyCRAC

Homepage:
https://bitbucket.org/sgrann/

Source Downloads:
73dff1be9488.tar.gz (8f968d1dca38aa2b3ac401ba8da70cef)
eadda2b95c34.tar.gz (c6b37913a6f7da123e3243166806aa56)

Download SlackBuild:
pyCRAC.tar.gz
pyCRAC.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

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See our HOWTO for instructions on how to use the contents of this repository.

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