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PEAKachu: a peak calling tool for CLIP/RIP-seq data

Bischler, Thorsten; Förstner, Konrad U.; Maticzka, Daniel; Wright, Patrick R.

PEAKachu is a peak calling tool for CLIP/RIP-seq data that can be used to identify targets and interaction sites of RNA-binding proteins. The tool is written in Python 3 and depends on several software packages for Python and R.

The following dependency package versions have been used for PEAKachu v.0.2.0: Python: Cython 0.29.13, numpy 1.18.5, scipy 1.3.1, matplotlib 3.3.1, pandas 0.25.1, biopython 1.77, pysam 0.16.0.1, bcbio-gff 0.6.6, statsmodels 0.10.1, numexpr 2.7.0, rpy2 3.1.0 R: edgeR 3.26.5, DESeq2 1.24.0
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