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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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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1147433", 
  "language": "eng", 
  "title": "Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC", 
  "issued": {
    "date-parts": [
      [
        2018, 
        1, 
        15
      ]
    ]
  }, 
  "abstract": "<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>", 
  "author": [
    {
      "family": "Gruber, Andreas J."
    }, 
    {
      "family": "Schmidt, Ralf"
    }, 
    {
      "family": "Ghosh, Souvik"
    }, 
    {
      "family": "Martin, Georges"
    }, 
    {
      "family": "Gruber, Andreas R."
    }, 
    {
      "family": "van Nimwegen, Erik"
    }, 
    {
      "family": "Zavolan, Mihaela"
    }
  ], 
  "type": "article", 
  "id": "1147433"
}
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