{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T09:36:24Z","timestamp":1774690584723,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,9,1]],"date-time":"2017-09-01T00:00:00Z","timestamp":1504224000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>As more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. These enable researchers to leverage vast datasets that would otherwise be difficult to obtain.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Snaptron is a search engine for summarized RNA sequencing data with a query planner that leverages R-tree, B-tree and inverted indexing strategies to rapidly execute queries over 146 million exon-exon splice junctions from over 70\u2009000 human RNA-seq samples. Queries can be tailored by constraining which junctions and samples to consider. Snaptron can score junctions according to tissue specificity or other criteria, and can score samples according to the relative frequency of different splicing patterns. We describe the software and outline biological questions that can be explored with Snaptron queries.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Documentation is at http:\/\/snaptron.cs.jhu.edu. Source code is at https:\/\/github.com\/ChristopherWilks\/snaptron and https:\/\/github.com\/ChristopherWilks\/snaptron-experiments with a CC BY-NC 4.0 license.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx547","type":"journal-article","created":{"date-parts":[[2017,8,31]],"date-time":"2017-08-31T15:15:02Z","timestamp":1504192502000},"page":"114-116","source":"Crossref","is-referenced-by-count":47,"title":["Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples"],"prefix":"10.1093","volume":"34","author":[{"given":"Christopher","family":"Wilks","sequence":"first","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"},{"name":"Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA"}]},{"given":"Phani","family":"Gaddipati","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA"}]},{"given":"Abhinav","family":"Nellore","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA"},{"name":"Department of Surgery, Oregon Health & Science University, Portland, OR, USA"},{"name":"Computational Biology Program, Oregon Health & Science University, Portland, OR, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2437-1976","authenticated-orcid":false,"given":"Ben","family":"Langmead","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"},{"name":"Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,9,1]]},"reference":[{"key":"2023020208303593100_btx547-B1","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nbt.3838","article-title":"Reproducible RNA-seq analysis using recount2","volume":"35","author":"Collado-Torres","year":"2017","journal-title":"Nat. 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