tomazc/icount repository overview

⁠iCount: protein-RNA interaction analysis

iCount is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions and generate:

• demultiplexed and adapter-trimmed FASTQ files,
• BAM files with mapped iCLIP reads,
• identified protein-RNA cross-linked sites, saved to BED files,
• peaks composed of statistically significant cross-linked sites, saved to BED files,
• clusters of significant cross-linked sites, saved to BED files,
• grouping of individual replicate experiments,
• RNAmap generation showing the positional distribution of cross-linked sites relative to genomic landmarks,
• kmer enrichment analysis,
• and other.

You may start with the tutorial⁠ or dive into the documentation⁠.

⁠Authors

iCount is developed and supported by Tomaž Curk⁠ from the Bioinformatics Laboratory⁠ at the University of Ljubljana⁠, Faculty of Computer and Information Science⁠ and in collaboration with the laboratory of Jernej Ule⁠.

The development started in late 2008 when Tomaž Curk and Gregor Rot wrote a first prototype of iCount. A lot has happend since then. For details and full acknowledgments, see the how to cite⁠ section in the documentation.

⁠Contributing

Contributions (pull requests) are welcome! Please submit your contributions by following the guidelines⁠.

⁠Reporting problems

Use the issues page⁠ to report issues and request enhancements. Before submitting, please check the list of already reported issues. Also, have a look at the FAQ⁠ to see if the problem has been addressed already.