J
Johannes Köster
Researcher at University of Duisburg-Essen
Publications - 52
Citations - 5569
Johannes Köster is an academic researcher from University of Duisburg-Essen. The author has contributed to research in topics: Workflow & Neuroblastoma. The author has an hindex of 17, co-authored 47 publications receiving 3563 citations. Previous affiliations of Johannes Köster include Centrum Wiskunde & Informatica & Technical University of Dortmund.
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Journal ArticleDOI
Snakemake--a scalable bioinformatics workflow engine.
Johannes Köster,Sven Rahmann +1 more
TL;DR: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.
Journal ArticleDOI
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning,Ryan K. Dale,Andreas Sjödin,Andreas Sjödin,Brad Chapman,Jillian Rowe,Christopher Tomkins-Tinch,Christopher Tomkins-Tinch,Renan Valieris,Johannes Köster,Johannes Köster +10 more
TL;DR: The present Bioconda, a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda, improves analysis reproducibility by allowing users to define isolated environments with defined software versions.
Journal ArticleDOI
Eleven grand challenges in single-cell data science
David Lähnemann,David Lähnemann,Johannes Köster,Johannes Köster,Ewa Szczurek,Davis J. McCarthy,Davis J. McCarthy,Stephanie C. Hicks,Mark D. Robinson,Catalina A. Vallejos,Catalina A. Vallejos,Kieran R Campbell,Kieran R Campbell,Niko Beerenwinkel,Niko Beerenwinkel,Ahmed Mahfouz,Ahmed Mahfouz,Luca Pinello,Luca Pinello,Pavel Skums,Alexandros Stamatakis,Alexandros Stamatakis,Camille Stephan Otto Attolini,Samuel Aparicio,Samuel Aparicio,Jasmijn A. Baaijens,Marleen Balvert,Marleen Balvert,Buys de Barbanson,Antonio Cappuccio,Giacomo Corleone,Bas E. Dutilh,Bas E. Dutilh,Maria Florescu,Victor Guryev,Rens Holmer,Katharina Jahn,Katharina Jahn,Thamar Jessurun Lobo,Emma M. Keizer,Indu Khatri,Szymon M. Kielbasa,Jan O. Korbel,Alexey M. Kozlov,Tzu Hao Kuo,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,Ion I. Mandoiu,John C. Marioni,John C. Marioni,John C. Marioni,Tobias Marschall,Tobias Marschall,Felix Mölder,Amir Niknejad,Lukasz Raczkowski,Marcel J. T. Reinders,Marcel J. T. Reinders,Jeroen de Ridder,Antoine-Emmanuel Saliba,Antonios Somarakis,Oliver Stegle,Oliver Stegle,Fabian J. Theis,Huan Yang,Alexander Zelikovsky,Alexander Zelikovsky,Alice C. McHardy,Benjamin J. Raphael,Sohrab P. Shah,Alexander Schönhuth,Alexander Schönhuth +71 more
TL;DR: This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years in single-cell data science.
Journal ArticleDOI
Sustainable data analysis with Snakemake.
Felix Mölder,Kim Philipp Jablonski,Kim Philipp Jablonski,Brice Letcher,Michael B Hall,Christopher Tomkins-Tinch,Christopher Tomkins-Tinch,Vanessa Sochat,Jan Forster,Jan Forster,Soohyun Lee,Sven Twardziok,Alexander Kanitz,Alexander Kanitz,Andreas Wilm,Manuel Holtgrewe,Sven Rahmann,Sven Nahnsen,Johannes Köster,Johannes Köster +19 more
TL;DR: It is shown how the popular workflow management system Snakemake can be used to guarantee reproducibility, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.
Journal ArticleDOI
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
Wei Li,Johannes Köster,Han Xu,Chen-Hao Chen,Tengfei Xiao,Jun Liu,Myles Brown,Myles Brown,X. Shirley Liu,X. Shirley Liu +9 more
TL;DR: MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions to iteratively estimate sgRNA knockout efficiency and gene essentiality.