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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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  <dc:creator>Gruber, Andreas J.</dc:creator>
  <dc:creator>Schmidt, Ralf</dc:creator>
  <dc:creator>Ghosh, Souvik</dc:creator>
  <dc:creator>Martin, Georges</dc:creator>
  <dc:creator>Gruber, Andreas R.</dc:creator>
  <dc:creator>van Nimwegen, Erik</dc:creator>
  <dc:creator>Zavolan, Mihaela</dc:creator>
  <dc:date>2018-01-15</dc:date>
  <dc:description>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. It connects the PAQR and KAPAC modules and includes as example input the mapped RNA-seq samples from the study of HNRNPC knock-down in HEK293 cells (originally published on the GEO database with the accession number GSE56010), available also from here: http://www.clipz.unibas.ch/RNAseq_HNRNPC_KD_study. 

PAQR is a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC infers position-dependent activities of sequence motifs on 3’ end processing from changes in poly(A) site usage between conditions.</dc:description>
  <dc:identifier>https://zenodo.org/record/1147433</dc:identifier>
  <dc:identifier>10.5281/zenodo.1147433</dc:identifier>
  <dc:identifier>oai:zenodo.org:1147433</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>info:eu-repo/grantAgreement/SNSF/Programmes/51NF40_141735/</dc:relation>
  <dc:relation>info:eu-repo/grantAgreement/SNSF/Project+funding/31003A_170216/</dc:relation>
  <dc:relation>doi:10.1101/195958</dc:relation>
  <dc:relation>doi:10.5281/zenodo.1147432</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://opensource.org/licenses/GPL-2.0</dc:rights>
  <dc:subject>Cleavage and polyadenylation</dc:subject>
  <dc:subject>APA</dc:subject>
  <dc:subject>quantification of poly(A) site usage</dc:subject>
  <dc:subject>regulators of polyadenylation</dc:subject>
  <dc:subject>HNRNPC</dc:subject>
  <dc:subject>RNA-seq</dc:subject>
  <dc:subject>Snakemake</dc:subject>
  <dc:title>Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>
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