The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update von Afgan, Enis, Baker, Dannon, Batut, Bérénice, van den Beek, Marius, Bouvier, Dave, Čech, Martin, Chilton, John, Clements, Dave, Coraor, Nate, Grüning, Björn A, Guerler, Aysam, Hillman-Jackson, Jennifer, Hiltemann, Saskia, Jalili, Vahid, Rasche, Helena, Soranzo, Nicola, Goecks, Jeremy, Taylor, James, Nekrutenko, Anton, Blankenberg, Daniel

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Bioconda: sustainable and comprehensive software distribution for the life sciences von Grüning, Björn, Dale, Ryan, Sjödin, Andreas, Chapman, Brad A., Rowe, Jillian, Tomkins-Tinch, Christopher H., Valieris, Renan, Köster, Johannes

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pyGenomeTracks: reproducible plots for multivariate genomic datasets von Lopez-Delisle, Lucille, Rabbani, Leily, Wolff, Joachim, Bhardwaj, Vivek, Backofen, Rolf, Gruening, Bjoern, Ramirez, Fidel, Manke, Thomas

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Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization von Wolff, Joachim, Bhardwaj, Vivek, Nothjunge, Stephan, Richard, Gautier, Renschler, Gina, Gilsbach, Ralf, Manke, Thomas, Backofen, Rolf, Ramírez, Fidel, Grüning, Björn A

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BioContainers: an open-source and community-driven framework for software standardization von da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset

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Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo von Gilsbach, Ralf, Schwaderer, Martin, Preissl, Sebastian, Grüning, Björn A., Kranzhöfer, David, Schneider, Pedro, Nührenberg, Thomas G., Mulero-Navarro, Sonia, Weichenhan, Dieter, Braun, Christian, Dreßen, Martina, Jacobs, Adam R., Lahm, Harald, Doenst, Torsten, Backofen, Rolf, Krane, Markus, Gelb, Bruce D., Hein, Lutz

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update von Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn A, Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael C, Ostrovsky, Alexander E, Mahmoud, Alexandru, Lonie, Andrew J, Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur C, DeSanto, Assunta D, Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn A, Langhorst, Bradley W, Carr, Bridget, Raubenolt, Bryan A, Hyde, Cameron J, Bromhead, Catherine J, Barnett, Christopher B, Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel J, Baker, Dannon, Bouvier, Dave, Clements, Dave, de Lima Morais, David A, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R, Cuccuru, Gianmauro, Corguillé, Gildas Le, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hotz, Hans-Rudolf, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J, Taylor, James P, Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John M, Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E, Tangaro, Marco Antonio, van den Beek, Marius, Čech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie C, Crusoe, Michael R, Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A, Moreno, Pablo A, Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D, Gu, Qiang, Weber, Ralf J M, Lazarus, Ross, Vorderman, Ruben H P, Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A, Gladman, Simon L, Leo, Simone, Mehta, Subina P, Griffin, Timothy J, Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K, Bacon, Wendi A, de Koning, Willem, Maier, Wolfgang

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Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease von Gilsbach, Ralf, Preissl, Sebastian, Grüning, Björn A., Schnick, Tilman, Burger, Lukas, Benes, Vladimir, Würch, Andreas, Bönisch, Ulrike, Günther, Stefan, Backofen, Rolf, Fleischmann, Bernd K., Schübeler, Dirk, Hein, Lutz

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Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis von Nührenberg, Thomas G, Stöckle, Jasmin, Marini, Federico, Zurek, Mark, Grüning, Björn A, Benes, Vladimir, Hein, Lutz, Neumann, Franz-Josef, Stratz, Christian, Cederqvist, Marco, Hochholzer, Willibald

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Transformer-based tool recommendation system in Galaxy von Kumar, Anup, Grüning, Björn, Backofen, Rolf

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Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers von Grüning, Björn A, Rasche, Eric, Rebolledo-Jaramillo, Boris, Eberhard, Carl, Houwaart, Torsten, Chilton, John, Coraor, Nate, Backofen, Rolf, Taylor, James, Nekrutenko, Anton

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Strategies for analyzing bisulfite sequencing data von Wreczycka, Katarzyna, Gosdschan, Alexander, Yusuf, Dilmurat, Grüning, Björn, Assenov, Yassen, Akalin, Altuna

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deepTools: a flexible platform for exploring deep-sequencing data von Ramírez, Fidel, Dündar, Friederike, Diehl, Sarah, Grüning, Björn A., Manke, Thomas

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DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes von Nothjunge, Stephan, Nührenberg, Thomas G., Grüning, Björn A., Doppler, Stefanie A., Preissl, Sebastian, Schwaderer, Martin, Rommel, Carolin, Krane, Markus, Hein, Lutz, Gilsbach, Ralf

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The bio.tools registry of software tools and data resources for the life sciences von Ison, Jon, Ienasescu, Hans, Chmura, Piotr, Rydza, Emil, Ménager, Hervé, Kalaš, Matúš, Schwämmle, Veit, Grüning, Björn, Beard, Niall, Lopez, Rodrigo, Duvaud, Severine, Stockinger, Heinz, Persson, Bengt, Vařeková, Radka Svobodová, Raček, Tomáš, Vondrášek, Jiří, Peterson, Hedi, Salumets, Ahto, Jonassen, Inge, Hooft, Rob, Nyrönen, Tommi, Valencia, Alfonso, Capella, Salvador, Gelpí, Josep, Zambelli, Federico, Savakis, Babis, Leskošek, Brane, Rapacki, Kristoffer, Blanchet, Christophe, Jimenez, Rafael, Oliveira, Arlindo, Vriend, Gert, Collin, Olivier, van Helden, Jacques, Løngreen, Peter, Brunak, Søren

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Fostering accessible online education using Galaxy as an e-learning platform von Serrano-Solano, Beatriz, Foell, Melanie C., Gallardo-Alba, Cristobal, Erxleben, Anika, Rasche, Helena, Hiltemann, Saskia, Fahrner, Matthias, Dunning, Mark J., Schulz, Marcel H., Scholtz, Beata, Clements, Dave, Nekrutenko, Anton, Batut, Berenice, Gruening, Bjoern A.

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Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation von Veil, Marina, Yampolsky, Lev Y, Grüning, Björn, Onichtchouk, Daria

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BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers von Bai, Jingwen, Bandla, Chakradhar, Guo, Jiaxin, Vera Alvarez, Roberto, Bai, Mingze, Vizcaíno, Juan Antonio, Moreno, Pablo, Grüning, Björn, Sallou, Olivier, Perez-Riverol, Yasset

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Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations von Schubert, Desirée, Bode, Claudia, Kenefeck, Rupert, Hou, Tie Zheng, Wing, James B, Kennedy, Alan, Bulashevska, Alla, Petersen, Britt-Sabina, Schäffer, Alejandro A, Grüning, Björn A, Unger, Susanne, Frede, Natalie, Baumann, Ulrich, Witte, Torsten, Schmidt, Reinhold E, Dueckers, Gregor, Niehues, Tim, Seneviratne, Suranjith, Kanariou, Maria, Speckmann, Carsten, Ehl, Stephan, Rensing-Ehl, Anne, Warnatz, Klaus, Rakhmanov, Mirzokhid, Thimme, Robert, Hasselblatt, Peter, Emmerich, Florian, Cathomen, Toni, Backofen, Rolf, Fisch, Paul, Seidl, Maximilian, May, Annette, Schmitt-Graeff, Annette, Ikemizu, Shinji, Salzer, Ulrich, Franke, Andre, Sakaguchi, Shimon, Walker, Lucy S K, Sansom, David M, Grimbacher, Bodo

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Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in Streptomyces von Präg, Andreas, Grüning, Björn A, Häckh, Matthias, Lüdeke, Steffen, Wilde, Marcel, Luzhetskyy, Andriy, Richter, Michael, Luzhetska, Marta, Günther, Stefan, Müller, Michael

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