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iCount 2.0.0.2

Computational pipeline for analysis of iCLIP data

Latest Version: 2.0.0.6b

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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](http://icount.readthedocs.io/en/latest/tutorial.html) or dive into the [documentation](http://icount.readthedocs.io/en/latest/index.html).

## Authors

iCount is developed and supported by [Tomaž Curk](http://curk.info) from the [Bioinformatics Laboratory](http://biolab.si) at the [University of Ljubljana](http://www.uni-lj.si), [Faculty of Computer and Information Science](http://www.fri.uni-lj.si) and in collaboration with the laboratory of [Jernej Ule](http://ulelab.info).

The development started in late 2008 when Tomaž Curk and Gregor Rot wrote a first prototype of iCount. In mid-2016, [Jure Zmrzlikar](https://github.com/JureZmrzlikar) from [Genialis](http://www.genialis.com) helped refactoring and improving the code, which is now available here. For details and full acknowledgments, see the [how to cite](http://icount.readthedocs.io/en/latest/cite.html) section in the documentation.

## Contributing

Contributions (pull requests) are welcome! Please submit your contributions by following the [guidelines](http://icount.readthedocs.io/en/latest/contributing.html).

## Reporting problems

Use the [issues page](https://github.com/tomazc/iCount/issues) to report issues and request enhancements. Before submitting, please check the list of already reported issues. Also, have a look at the [FAQ](http://icount.readthedocs.io/en/latest/faq.html) to see if the problem has been addressed already.

 
File Type Py Version Uploaded on Size
iCount-2.0.0.2.tar.gz (md5) Source 2017-07-16 123KB