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Visualizing next-generation sequencing data with JBrowse.
Westesson O, Skinner M, Holmes I. Westesson O, et al. Among authors: holmes i. Brief Bioinform. 2013 Mar;14(2):172-7. doi: 10.1093/bib/bbr078. Epub 2012 Mar 12. Brief Bioinform. 2013. PMID: 22411711 Free PMC article.
JBrowse: a dynamic web platform for genome visualization and analysis.
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH. Buels R, et al. Genome Biol. 2016 Apr 12;17:66. doi: 10.1186/s13059-016-0924-1. Genome Biol. 2016. PMID: 27072794 Free PMC article.
Apollo: Democratizing genome annotation.
Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE. Dunn NA, et al. PLoS Comput Biol. 2019 Feb 6;15(2):e1006790. doi: 10.1371/journal.pcbi.1006790. eCollection 2019 Feb. PLoS Comput Biol. 2019. PMID: 30726205 Free PMC article.
Cram-JS: reference-based decompression in node and the browser.
Buels R, Dider S, Diesh C, Robinson J, Holmes I. Buels R, et al. Among authors: holmes i. Bioinformatics. 2019 Nov 1;35(21):4451-4452. doi: 10.1093/bioinformatics/btz384. Bioinformatics. 2019. PMID: 31099383 Free PMC article.
JBrowseR: an R interface to the JBrowse 2 genome browser.
Hershberg EA, Stevens G, Diesh C, Xie P, De Jesus Martinez T, Buels R, Stein L, Holmes I. Hershberg EA, et al. Among authors: holmes i. Bioinformatics. 2021 Nov 5;37(21):3914-3915. doi: 10.1093/bioinformatics/btab459. Bioinformatics. 2021. PMID: 34196689 Free PMC article.
JBrowse Jupyter: a Python interface to JBrowse 2.
De Jesus Martinez T, Hershberg EA, Guo E, Stevens GJ, Diesh C, Xie P, Bridge C, Cain S, Haw R, Buels RM, Stein LD, Holmes IH. De Jesus Martinez T, et al. Bioinformatics. 2023 Jan 1;39(1):btad032. doi: 10.1093/bioinformatics/btad032. Bioinformatics. 2023. PMID: 36648320 Free PMC article.
JBrowse 2: a modular genome browser with views of synteny and structural variation.
Diesh C, Stevens GJ, Xie P, De Jesus Martinez T, Hershberg EA, Leung A, Guo E, Dider S, Zhang J, Bridge C, Hogue G, Duncan A, Morgan M, Flores T, Bimber BN, Haw R, Cain S, Buels RM, Stein LD, Holmes IH. Diesh C, et al. Among authors: holmes ih. Genome Biol. 2023 Apr 17;24(1):74. doi: 10.1186/s13059-023-02914-z. Genome Biol. 2023. PMID: 37069644 Free PMC article.
Setting up the JBrowse genome browser.
Skinner ME, Holmes IH. Skinner ME, et al. Curr Protoc Bioinformatics. 2010 Dec;Chapter 9:Unit 9.13. doi: 10.1002/0471250953.bi0913s32. Curr Protoc Bioinformatics. 2010. PMID: 21154710 Free PMC article.
276 results