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

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


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  <identifier identifierType="DOI">10.5281/zenodo.4669966</identifier>
  <creators>
    <creator>
      <creatorName>Bischler, Thorsten</creatorName>
      <givenName>Thorsten</givenName>
      <familyName>Bischler</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9288-9481</nameIdentifier>
      <affiliation>University of Wuerzburg</affiliation>
    </creator>
    <creator>
      <creatorName>Förstner, Konrad U.</creatorName>
      <givenName>Konrad U.</givenName>
      <familyName>Förstner</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1481-2996</nameIdentifier>
      <affiliation>ZB MED</affiliation>
    </creator>
    <creator>
      <creatorName>Maticzka, Daniel</creatorName>
      <givenName>Daniel</givenName>
      <familyName>Maticzka</familyName>
    </creator>
    <creator>
      <creatorName>Wright, Patrick R.</creatorName>
      <givenName>Patrick R.</givenName>
      <familyName>Wright</familyName>
    </creator>
  </creators>
  <titles>
    <title>PEAKachu: a peak calling tool for CLIP/RIP-seq data</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>Peak calling</subject>
    <subject>CLIP-seq</subject>
    <subject>RIP-seq</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-04-07</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4669966</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/tbischler/PEAKachu/tree/v0.2.0</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4669965</relatedIdentifier>
  </relatedIdentifiers>
  <version>v0.2.0</version>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/ISC">ISC License</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;/p&gt;</description>
    <description descriptionType="Other">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</description>
  </descriptions>
</resource>
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