Lucille Lopez-Delisle1, Leily Rabbani2, Joachim Wolff3, Vivek Bhardwaj2, Rolf Backofen3,4, Björn Grüning3, Fidel Ramírez2, Thomas Manke2. 1. UPDUB, ISREC Department, School of Life Sciences (SV), EPFL, 1015 Lausanne, Switzerland. 2. Bioinformatics Group, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany. 3. Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany. 4. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.
Abstract
MOTIVATION: Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using a vector graphic software. RESULTS: pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks. It enables a reproducible and standardized generation of highly customizable and publication ready images. AVAILABILITY AND IMPLEMENTATION: PGT is available through a graphical interface on https://usegalaxy.eu and through the command line. It is provided on conda via the bioconda channel, on pip and it is openly developed on github: https://github.com/deeptools/pyGenomeTracks. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using a vector graphic software. RESULTS: pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks. It enables a reproducible and standardized generation of highly customizable and publication ready images. AVAILABILITY AND IMPLEMENTATION: PGT is available through a graphical interface on https://usegalaxy.eu and through the command line. It is provided on conda via the bioconda channel, on pip and it is openly developed on github: https://github.com/deeptools/pyGenomeTracks. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: David De Sa Nogueira; Romain Bourdy; Rafael Alcala-Vida; Dominique Filliol; Virginie Andry; Yannick Goumon; Jean Zwiller; Pascal Romieu; Karine Merienne; Mary C Olmstead; Katia Befort Journal: Mol Neurobiol Date: 2022-01-15 Impact factor: 5.590
Authors: Katerina Cermakova; Jonas Demeulemeester; Vanda Lux; Monika Nedomova; Seth R Goldman; Eric A Smith; Pavel Srb; Rozalie Hexnerova; Milan Fabry; Marcela Madlikova; Magdalena Horejsi; Jan De Rijck; Zeger Debyser; Karen Adelman; H Courtney Hodges; Vaclav Veverka Journal: Science Date: 2021-11-25 Impact factor: 47.728
Authors: Jacob W Freimer; Oren Shaked; Sahin Naqvi; Nasa Sinnott-Armstrong; Arwa Kathiria; Christian M Garrido; Amy F Chen; Jessica T Cortez; William J Greenleaf; Jonathan K Pritchard; Alexander Marson Journal: Nat Genet Date: 2022-07-11 Impact factor: 41.307
Authors: Simon Linder; Marlous Hoogstraat; Suzan Stelloo; Nils Eickhoff; Karianne Schuurman; Hilda de Barros; Maartje Alkemade; Elise M Bekers; Tesa M Severson; Joyce Sanders; Chia-Chi Flora Huang; Tunc Morova; Umut Berkay Altintas; Liesbeth Hoekman; Yongsoo Kim; Sylvan C Baca; Martin Sjöström; Anniek Zaalberg; Dorine C Hintzen; Jeroen de Jong; Roelof J C Kluin; Iris de Rink; Claudia Giambartolomei; Ji-Heui Seo; Bogdan Pasaniuc; Maarten Altelaar; René H Medema; Felix Y Feng; Amina Zoubeidi; Matthew L Freedman; Lodewyk F A Wessels; Lisa M Butler; Nathan A Lack; Henk van der Poel; Andries M Bergman; Wilbert Zwart Journal: Cancer Discov Date: 2022-09-02 Impact factor: 38.272
Authors: Le Xiong; Erik A Tolen; Jinmi Choi; Sergiy Velychko; Livia Caizzi; Taras Velychko; Kenjiro Adachi; Caitlin M MacCarthy; Michael Lidschreiber; Patrick Cramer; Hans R Schöler Journal: Elife Date: 2022-05-27 Impact factor: 8.713
Authors: Andrew Ryan Passer; Shelly Applen Clancey; Terrance Shea; Márcia David-Palma; Anna Floyd Averette; Teun Boekhout; Betina M Porcel; Minou Nowrousian; Christina A Cuomo; Sheng Sun; Joseph Heitman; Marco A Coelho Journal: Elife Date: 2022-06-17 Impact factor: 8.713