{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T19:24:19Z","timestamp":1778009059994,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011477","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T00:00:00Z","timestamp":1694736000000}}],"reference-count":13,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T00:00:00Z","timestamp":1693872000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the National Key Research and Development Program of China, Stem Cell and Translational Research","award":["2022YFA1105200"],"award-info":[{"award-number":["2022YFA1105200"]}]},{"DOI":"10.13039\/501100001809","name":"the National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82303975"],"award-info":[{"award-number":["82303975"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"the National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82273117"],"award-info":[{"award-number":["82273117"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100010031","name":"Postdoctoral Research Foundation of China","doi-asserted-by":"publisher","award":["2022TQ0226"],"award-info":[{"award-number":["2022TQ0226"]}],"id":[{"id":"10.13039\/501100010031","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Post-Doctor Research Project, West China Hospital, Sichuan University","award":["2023HXBH100"],"award-info":[{"award-number":["2023HXBH100"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Here, we introduce Trackplot, a Python package for generating publication-quality visualization by a programmable and interactive web-based approach. Compared to the existing versions of programs generating sashimi plots, Trackplot offers a versatile platform for visually interpreting genomic data from a wide variety of sources, including gene annotation with functional domain mapping, isoform expression, isoform structures identified by scRNA-seq and long-read sequencing, as well as chromatin accessibility and architecture without any preprocessing, and also offers a broad degree of flexibility for formats of output files that satisfy the requirements of major journals. The Trackplot package is an open-source software which is freely available on Bioconda (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/anaconda.org\/bioconda\/trackplot\" xlink:type=\"simple\">https:\/\/anaconda.org\/bioconda\/trackplot<\/jats:ext-link>\n                    ), Docker (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/hub.docker.com\/r\/ygidtu\/trackplot\" xlink:type=\"simple\">https:\/\/hub.docker.com\/r\/ygidtu\/trackplot<\/jats:ext-link>\n                    ), PyPI (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/pypi.org\/project\/sashimi.py\/\" xlink:type=\"simple\">https:\/\/pypi.org\/project\/trackplot\/<\/jats:ext-link>\n                    ) and GitHub (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ygidtu\/trackplot\" xlink:type=\"simple\">https:\/\/github.com\/ygidtu\/trackplot<\/jats:ext-link>\n                    ), and a built-in web server for local deployment is also provided.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1011477","type":"journal-article","created":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T13:31:20Z","timestamp":1693920680000},"page":"e1011477","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Trackplot: A flexible toolkit for combinatorial analysis of genomic data"],"prefix":"10.1371","volume":"19","author":[{"given":"Yiming","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8175-2508","authenticated-orcid":true,"given":"Ran","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lunxu","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lu","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6324-6134","authenticated-orcid":true,"given":"Yuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2023,9,5]]},"reference":[{"key":"pcbi.1011477.ref001","article-title":"Alternative splicing as a source of phenotypic diversity","author":"CJ Wright","year":"2022","journal-title":"Nat Rev Genet"},{"issue":"5","key":"pcbi.1011477.ref002","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets","volume":"161","author":"EZ Macosko","year":"2015","journal-title":"Cell"},{"issue":"1","key":"pcbi.1011477.ref003","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","article-title":"The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community","volume":"17","author":"M Jain","year":"2016","journal-title":"Genome Biol"},{"issue":"14","key":"pcbi.1011477.ref004","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1093\/bioinformatics\/btv034","article-title":"Quantitative visualization of alternative exon expression from RNA-seq data","volume":"31","author":"Y Katz","year":"2015","journal-title":"Bioinformatics"},{"issue":"8","key":"pcbi.1011477.ref005","doi-asserted-by":"crossref","first-page":"e1006360","DOI":"10.1371\/journal.pcbi.1006360","article-title":"ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.","volume":"14","author":"D Garrido-Martin","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"7","key":"pcbi.1011477.ref006","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1093\/bioinformatics\/btt733","article-title":"SplicePlot: a utility for visualizing splicing quantitative trait loci","volume":"30","author":"E Wu","year":"2014","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1011477.ref007","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.","volume":"14","author":"H Thorvaldsdottir","year":"2013","journal-title":"Brief Bioinform"},{"issue":"16","key":"pcbi.1011477.ref008","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1011477.ref009","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/nar\/gky092","article-title":"UniProt: the universal protein knowledgebase","volume":"46","author":"T. UniProt Consortium","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pcbi.1011477.ref010","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022.","volume":"50","author":"F Cunningham","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pcbi.1011477.ref011","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/s41422-020-00451-z","article-title":"Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma","volume":"31","author":"X Wang","year":"2021","journal-title":"Cell Res"},{"issue":"11","key":"pcbi.1011477.ref012","doi-asserted-by":"crossref","first-page":"5586","DOI":"10.1093\/nar\/gkv429","article-title":"Generation of functionally distinct isoforms of PTBP3 by alternative splicing and translation initiation","volume":"43","author":"LY Tan","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"pcbi.1011477.ref013","doi-asserted-by":"crossref","first-page":"e66","DOI":"10.1093\/nar\/gkac167","article-title":"SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming","volume":"50","author":"R Zhou","year":"2022","journal-title":"Nucleic Acids Res"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1011477","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T00:00:00Z","timestamp":1694736000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011477","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T13:45:49Z","timestamp":1694785549000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011477"}},"subtitle":[],"editor":[{"given":"Mark","family":"Ziemann","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,9,5]]},"references-count":13,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2023,9,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1011477","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.11.02.514803","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,5]]}}}