Computational pipeline for analysis of iCLIP data
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.
Contributions (pull requests) are welcome! Please submit your contributions by following the guidelines.