software . 2018

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;
Open Source English
  • Published: 15 Jan 2018
  • Publisher: Zenodo
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> <p>PAQR is&nbsp;a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC&nbsp;infers p...
Subjects
free text keywords: Cleavage and polyadenylation, APA, quantification of poly(A) site usage, regulators of polyadenylation, HNRNPC, RNA-seq, Snakemake
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Zenodo
Software . 2018
Provider: Datacite
Zenodo
Software . 2018
Provider: Datacite
Zenodo
Software . 2018
Provider: Zenodo
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software . 2018

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;