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Software . 2021
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Software . 2021
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Software . 2021
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PEAKachu: a peak calling tool for CLIP/RIP-seq data

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 07 Apr 2021Publisher:Zenodo
Authors: Bischler, Thorsten; Förstner, Konrad U.; Maticzka, Daniel; Wright, Patrick R.;
Code repository: https://github.com/tbischler/PEAKachu/tree/v0.2.0

doi: 10.5281/zenodo.4669965 , 10.5281/zenodo.4669966

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

Abstract

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

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.

Related Organizations
Keywords

RIP-seq, CLIP-seq, Peak calling

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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