Software

 

• wavClusteR:

Current version
0.99.2 (beta, in review for BioC submission)

Description
This package provides functions for the analysis of Next-Generation Sequencing data obtained from substitution inducing experimental procedures (e.g. PAR-CLIP, BisSeq). The implemented workflow consists of a two-component mixture model, identifying experimentally affected substitution frequencies, and a wavelet-based peak calling procedure. The two steps of the workflow can be regarded as modular and have been built such that they are easily exchangeable if required. To speed up computations, key functions support parallel multicore computing.

 

Download

wavClusteR_0.99.2.tar.gz

wavClusteR-manual.pdf

wavCluster_vignette.pdf

 

Authors

Federico Comoglio (federico.comoglio@bsse.ethz.ch)

Cem Sievers (cem.sievers@bsse.ethz.ch)

 

Citation

If you are using wavClusteR for your analysis, please cite it as:
Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R.
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.
Nucleic Acids Res. 2012 Jul 28.