iCount 2.0.0

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.