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Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC

Gruber, Andreas J.; Schmidt, Ralf; Ghosh, Souvik; Martin, Georges; Gruber, Andreas R.; van Nimwegen, Erik; Zavolan, Mihaela


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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>This archive contains the Snakemake workflow as it was used in the Genome Biology publication. The workflow is provided in a self-contained environment that only requires Conda and Snakemake to be executed.&nbsp;It&nbsp;connects the PAQR and KAPAC modules and includes as example&nbsp;input the&nbsp;mapped RNA-seq samples from the study of HNRNPC knock-down in HEK293 cells (originally published on the GEO database with the accession number&nbsp;GSE56010), available also from here:&nbsp;http://www.clipz.unibas.ch/RNAseq_HNRNPC_KD_study.&nbsp;</p>\n\n<p>PAQR is&nbsp;a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC&nbsp;infers position-dependent activities of sequence motifs on 3&rsquo; end processing from changes in poly(A) site usage between conditions.</p>", 
  "license": "https://opensource.org/licenses/GPL-2.0", 
  "creator": [
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@id": "https://orcid.org/0000-0001-7664-4257", 
      "@type": "Person", 
      "name": "Gruber, Andreas J."
    }, 
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@type": "Person", 
      "name": "Schmidt, Ralf"
    }, 
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@type": "Person", 
      "name": "Ghosh, Souvik"
    }, 
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@type": "Person", 
      "name": "Martin, Georges"
    }, 
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@type": "Person", 
      "name": "Gruber, Andreas R."
    }, 
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@type": "Person", 
      "name": "van Nimwegen, Erik"
    }, 
    {
      "affiliation": "Computational and Systems Biology, Biozentrum, University of Basel", 
      "@id": "https://orcid.org/0000-0002-8832-2041", 
      "@type": "Person", 
      "name": "Zavolan, Mihaela"
    }
  ], 
  "url": "https://zenodo.org/record/1147433", 
  "citation": [
    {
      "@id": "https://doi.org/10.1101/195958", 
      "@type": "CreativeWork"
    }
  ], 
  "datePublished": "2018-01-15", 
  "keywords": [
    "Cleavage and polyadenylation", 
    "APA", 
    "quantification of poly(A) site usage", 
    "regulators of polyadenylation", 
    "HNRNPC", 
    "RNA-seq", 
    "Snakemake"
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.1147433", 
  "@id": "https://doi.org/10.5281/zenodo.1147433", 
  "@type": "SoftwareSourceCode", 
  "name": "Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC"
}
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