The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Autor: Abueg, L.A.L., Afgan, E., Allart, O., Awan, A.H., Bacon, W.A., Baker, D., Bassetti, M., Batut, B., Bernt, M., Blankenberg, D., Bombarely, A., Bretaudeau, A., Bromhead, C.J., Burke, M.L., Capon, P.K., Čech, M., Chavero-Díez, M., Chilton, J.M., Collins, T.J., Coppens, F., Coraor, N., Cuccuru, G., Cumbo, F., Davis, J., De Geest, P.F., de Koning, W., Demko, M., DeSanto, A., Domínguez Begines, J.M., Doyle, M.A., Droesbeke, B., Erxleben-Eggenhofer, A., Föll, M.C., Formenti, G., Fouilloux, A., Gangazhe, R., Genthon, T., Goecks, J., Gonzalez Beltran, A.N., Goonasekera, N.A., Goué, N., Griffin, T.J., Grüning, B.A., Guerler, A., Gundersen, S., Gustafsson, O.J.R., Hall, C., Harrop, T.W., Hecht, H., Heidari, A., Heisner, T., Heyl, F., Hiltemann, S., Hotz, H.-R., Hyde, C.J., Jagtap, P.D., Jakiela, J., Johnson, J.E., Joshi, J., Jossé, M., Jum'ah, Khaled, Kalaš, M., Kamieniecka, Katarzyna, Kayikcioglu, T., Konkol, M., Kostrykin, L., Kucher, N., Kumar, A., Kuntz, M., Lariviere, D., Lazarus, R., Le Bras, Y., Le Corguillé, G., Lee, J., Leo, S., Liborio, L., Libouban, R., López Tabernero, D., Lopez-Delisle, L., Los, L.S., Mahmoud, A., Makunin, I., Marin, P., Mehta, S., Mok, W., Moreno, P.A., Morier-Genoud, F., Mosher, S., Müller, T., Nasr, E., Nekrutenko, A., Nelson, T.M., Oba, A.J., Ostrovsky, A., Polunina, P.V., Poterlowicz, Krzysztof, Price, E.J., Price, G.R., Rasche, H., Raubenolt, B., Royaux, C., Sargent, L., Savage, M.T., Savchenko, V., Savchenko, D., Schatz, M.C., Seguineau, P., Serrano-Solano, B., Soranzo, N., Srikakulam, S.K., Suderman, K., Syme, A.E., Tangaro, M.A., Tedds, J.A., Tekman, M., Thang, W.C.M., Thanki, A.S., Uhl, M., van den Beek, M., Varshney, D., Vessio, J., Videm, P., Von Kuster, G., Watson, G.R., Whitaker-Allen, N., Winter, U., Wolstencroft, M., Zambelli, F., Zierep, P., Zoabi, R.

Yes
Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool

Externí odkaz: http://hdl.handle.net/10454/19930

A community effort to create standards for evaluating tumor subclonal reconstruction

Autor: Salcedo, A., Tarabichi, M., Espiritu, S.M.G., Deshwar, A.G., David, M., Wilson, N.M., Dentro, S., Wintersinger, J.A., Liu, L.Y., Ko, M., Sivanandan, S., Zhang, H., Zhu, K., Ou Yang, T.-H., Chilton, J.M., Buchanan, A., Lalansingh, C.M., P’ng, C., Anghel, C.V., Umar, I., Lo, B., Zou, W., Jha, A., Huang, T., Yang, T.-P., Peifer, M., Sahinalp, C., Malikic, S., Vázquez-García, I., Mustonen, V., Yang, H.-T., Lee, K.-R., Ji, Y., Sengupta, Subhajit, Rudewicz, J., Nikolski, M., Schaeverbeke, Q., Yuan, K., Markowetz, F., Macintyre, G., Cmero, M., Chaudhary, B., Leshchiner, I., Livitz, D., Getz, G., Loher, P., Yu, K., Wang, W., Zhu, H., Simpson, J.T., Stuart, J.M., Anastassiou, D., Guan, Y., Ewing, A.D., Ellrott, K., Wedge, D.C., Morris, Q., Van Loo, P., Boutros, P.C.

Publikováno v: Nature biotechnology
Salcedo, A, Tarabichi, M, Espiritu, S M G, Deshwar, A G, David, M, Wilson, N M, Dentro, S, Wintersinger, J A, Liu, L Y, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, T-H, Chilton, J M, Buchanan, A, Lalansingh, C M, P’ng, C, Anghel, C V, Umar, I, Lo, B, Zou, W, Jha, A, Huang, T, Yang, T-P, Peifer, M, Sahinalp, C, Malikic, S, Vázquez-García, I, Mustonen, V, Yang, H-T, Lee, K-R, Ji, Y, Sengupta, S, Rudewicz, J, Nikolski, M, Schaeverbeke, Q, Yuan, K, Markowetz, F, Macintyre, G, Cmero, M, Chaudhary, B, Leshchiner, I, Livitz, D, Getz, G, Loher, P, Yu, K, Wang, W, Zhu, H, Simpson, J T, Stuart, J M, Anastassiou, D, Guan, Y, Ewing, A D, Ellrott, K, Wedge, D C, Morris, Q, Van Loo, P & Boutros, P C 2020, ' A community effort to create standards for evaluating tumor subclonal reconstruction ', Nature biotechnology, vol. 38, pp. 97-107 . https://doi.org/10.1038/s41587-019-0364-z
Nature Biotechnology
Nature Biotechnology, Nature Publishing Group, 2020, 38 (1), pp.97-107. ⟨10.1038/s41587-019-0364-z⟩

Tumor DNA sequencing data can be interpreted by computational methods that analyse genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and res

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0504e7284bebb5f3215ef901ac368c8c
https://doi.org/10.1038/s41587-019-0364-z

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