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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.


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.


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.

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