September 13, 2021 Preprint Open Access

Rosa Hernansaiz-Ballesteros; Christian H. Holland; Aurelien Dugourd; Julio Saez-Rodriguez

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  <identifier identifierType="DOI">10.5281/zenodo.5779097</identifier>
  <creators>
    <creator>
      <creatorName>Rosa Hernansaiz-Ballesteros</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8536-8848</nameIdentifier>
      <affiliation>Heidelberg University</affiliation>
    </creator>
    <creator>
      <creatorName>Christian H. Holland</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-3060-5786</nameIdentifier>
      <affiliation>Heidelberg University</affiliation>
    </creator>
    <creator>
      <creatorName>Aurelien Dugourd</creatorName>
      <affiliation>Heidelberg University</affiliation>
    </creator>
    <creator>
      <creatorName>Julio Saez-Rodriguez</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8552-8976</nameIdentifier>
      <affiliation>Heidelberg University</affiliation>
    </creator>
  </creators>
  <titles>
    <title>FUNKI: Interactive functional footprint-based analysis of omics data</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>funcional analysis</subject>
    <subject>omics</subject>
    <subject>shinyR</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-09-13</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Preprint"/>
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    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5779097</alternateIdentifier>
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    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo">https://arxiv.org/abs/2109.05796</relatedIdentifier>
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  <version>V2.0.0</version>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/AGPL-3.0">GNU Affero General Public License v3.0</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription factors and kinases based on known regulated targets, that we call footprints. Then the molecular paths driving these activities can be estimated using causal reasoning on large signaling networks. Results: We have developed FUNKI, a FUNctional toolKIt for footprint analysis. It provides a user-friendly interface for an easy and fast analysis of several omics data, either from bulk or single-cell experiments. FUNKI also features different options to visualise the results and run post-analyses, and is mirrored as a scripted version in R. Availability: FUNKI is a free and open-source application built on R and Shiny, available in GitHub at https://github.com/saezlab/ShinyFUNKI under GNU v3.0 license and accessible also in https://saezlab.shinyapps.io/funki/ Contact: pub.saez@uni-heidelberg.de Supplementary information: We provide data examples within the app, as well as extensive information about the different variables to select, the results, and the different plots in the help page.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/100010661</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/826121/">826121</awardNumber>
      <awardTitle>individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology</awardTitle>
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