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3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.

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kokonech/EPN_HiC_analysis

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Tools found in the code: circlize, ComplexHeatmap, DESeq2, ggplot2, SAMtools, tidyverse

Overview

Authors: Konstantin Okonechnikov, Aylin Camgöz, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Hübner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin Sikkink, Monika Mauermann, Edwin F. Juarez, Anne Jenseit, James T. Robinson, Kristian W. Pajtler, Till Milde
and 31 other authorsNatalie Jäger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G. Coufal, Michael Levy, Denise Malicki, Charlotte Hobbs, Stephen Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J. Wechsler-Reya, Tom Belle Davidson, Jennifer Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A. Kumar, Michael D. Taylor, Jeremy Rich, Frank Buchholz, Jill P. Mesirov, Stefan M. Pfister, Ferhat Ay, Jesse R. Dixon, Marcel Kool, Lukas Chavez
Published: 21 April 2023
Type: Research article
Status: code verified (how the code is found and verified)
License: CC BY
Institutions: German Cancer Research Center (Germany), Hopp Children's Cancer Center Heidelberg (Germany), Deutsches Konsortium für Translationale Krebsforschung (Germany), Helmholtz-Zentrum Dresden-Rossendorf (Germany), National Center for Tumor Diseases (Germany), University Hospital Carl Gustav Carus (Germany), Nationales Centrum für Tumorerkrankungen Dresden (Germany), German Cancer Research Center (DKFZ) Dresden (Germany), Technische Universität Dresden (Germany), University of California San Diego (United States), Sanford Consortium for Regenerative Medicine (United States), La Jolla Institute for Immunology (United States), Salk Institute for Biological Studies (United States), Stanford University (United States), Max Planck Institute for Molecular Genetics (Germany), Charité – Universitätsmedizin Berlin (Germany), Arima Genomics (United States) (United States), Heidelberg University (Germany), University Hospital Heidelberg (Germany), Rady Children's Hospital-San Diego (United States), Rady Children's Institute for Genomic Medicine (United States), NYU Langone Health (United States), NYU Langone’s Laura and Isaac Perlmutter Cancer Center (United States), New York University (United States), Sanford Burnham Prebys Medical Discovery Institute (United States), Children's Hospital Los Angeles (United States), Essen University Hospital (Germany), University of Toronto (Canada), Hospital for Sick Children (Canada), German Cancer Consortium (DKTK) Dresden (Germany), Moores Cancer Center (United States), Princess Máxima Center (Netherlands)

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