trxtools
trxtools was initiated as a storage for functions and scripts using in Turowski Lab to conduct various bioinformatics. There is no intention to create a comprehensive package that can be operated by non-experienced user, but some scripts are easy to run for everyone. Importantly the package provides useful functions for skilled individuals.
Major focus is put on postprocessing of high-troughput sequencing data originating from the followin methods:
CRAC/CLIP
RNA-seq
tRNA-seq
NET-seq
ChIP-seq
Some functions in the package use a specific file naming system:
'expID', 'expDate', 'protein', 'condition1', 'condition2', 'condition3'
i.e. C123_JK050420_POLR2A-FLAG_wt_arsenite30min will be used for an experiment C123 conducted by a person JK on 020420. This is puldown with POLR2A-FLAG in wt cells after arsenite30min