Skip to main content

Computational pipeline for analysis of iCLIP data

Project description

Build Status PyPI version codecov Codacy Badge CLA assistant Docker Automated build Documentation Status

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. In mid-2016, Jure Zmrzlikar from Genialis helped refactoring and improving the code, which is now available here. 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.

Project details

Release history Release notifications

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
iCount-2.0.0.tar.gz (128.8 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page