Anup Kumar
University of Freiburg
10 Papers
7 Citations
Anup Kumar is an academic researcher from University of Freiburg. The author has contributed to research in topics: Computer science & Deep learning. The author has an hindex of 2, co-authored 6 publications.
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Papers
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Enis Afgan,Anton Nekrutenko,Björn Grüning,Daniel Blankenberg,Jeremy Goecks,Michael C. Schatz,Alexander E. Ostrovsky,Alexandru Mahmoud,Andrew Lonie,Anna Syme,Anne Fouilloux,Anthony Bretaudeau,Anup Kumar,Arthur C. Eschenlauer,Assunta D. Desanto,Aysam Guerler,Beatriz Serrano-Solano,Bérénice Batut,Bradley W. Langhorst,Bridget Carr,Bryan Raubenolt,Cameron J. Hyde,Catherine J. Bromhead,Christopher B. Barnett,Coline Royaux,Cristóbal L. García Gallardo,Daniel Fornika,Dannon Baker,Dave Bouvier,Dave Clements,David A. de Lima Morais,David Lopez Tabernero,Delphine Larivière,E. Nasr,Federico Zambelli,Florian Heyl,Fotis Psomopoulos,Frederik Coppens,Gareth Price,Gianmauro Cuccuru,Gildas Le Corguillé,Gregory Von Kuster,Gulsum Gudukbay,Helena Rasche,Hans-Rudolf Hotz,Ignacio Eguinoa,Igor V. Makunin,Isuru Ranawaka,James Taylor,Jayadev Joshi,Jennifer Hillman-Jackson,John Chilton,Kaivan Kamali,Keith Suderman,Krzysztof Poterlowicz,Yvan Le Bras,Lucille Lopez-Delisle,Luke Sargent,Madeline E. Bassetti,M. A. Tangaro,Marius van den Beek,Martin Čech,Matthias Bernt,Matthias Fahrner,Mehmet Tekman,Melanie Föll,Michael R. Crusoe,Miguel Angel Roncoroni,N. K. Kucher,Nathaniel Coraor,Nicholas Stoler,Nick Rhodes,Nicola Soranzo,Niko Pinter,Nuwan Goonasekera,Pablo Moreno,Pavankumar Videm,Petera Melanie,Pietro Mandreoli,Pratik D. Jagtap,Qiang Gu,Ralf J. M. Weber,Ross Lazarus,Ruben H.P. Vorderman,Saskia Hiltemann,Sergey Golitsynskiy,Shilpa Garg,Simon Bray,Simon Gladman,Simone Leo,Subina Mehta,Timothy J. Griffin,Vahid Jalili,Yves Vandenbrouck,Vi-Kwei Wen,Vijaykrishna Nagampalli,W. Bacon,W. L. De Koning,Wolf-Martin Maier,P. J. Briggs +99 more
TL;DR: Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools.
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform.
TL;DR: The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins, based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis.
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine.
Qiang Gu,Anup Kumar,Simon Bray,Allison L. Creason,Alireza Khanteymoori,Vahid Jalili,Björn Grüning,Jeremy Goecks +7 more
TL;DR: Galaxy-ML as discussed by the authors is a biomedical computational workbench used by tens of thousands of scientists across the world, with a suite of tools for all aspects of supervised machine learning for biomedical data analysis.
Tool recommender system in Galaxy using deep learning
TL;DR: A model is created to recommend tools by analysing workflows, composed by researchers on the European Galaxy server, using a deep learning approach to make creating workflows easier, faster and less error-prone.
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
TL;DR: ChiRA as mentioned in this paper is a generic framework for sensitive annotation of these chimeric reads, which in turn can be used to predict the sequenced hybrids, in which the reference loci are grouped on the basis of aligned common reads and quantification improved the handling of the multi-mapped reads in contrast to common strategies such as the selection of the longest hit or a random choice among all hits.