{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:04Z","timestamp":1772138044002,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,3,11]],"date-time":"2021-03-11T00:00:00Z","timestamp":1615420800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Nanyang Technological University Start-Up Grant"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>There are now more than two million RNA sequencing experiments for plants, animals, bacteria and fungi publicly available, allowing us to study gene expression within and across species and kingdoms. However, the tools allowing the download, quality control and annotation of this data for more than one species at a time are currently missing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To remedy this, we present the Large-Scale Transcriptomic Analysis Pipeline in Kingdom of Life (LSTrAP-Kingdom) pipeline, which we used to process 134\u00a0521 RNA-seq samples, achieving \u223c12\u00a0000 processed samples per day. Our pipeline generated quality-controlled, annotated gene expression matrices that rival the manually curated gene expression data in identifying functionally related genes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>LSTrAP-Kingdom is available from: https:\/\/github.com\/wirriamm\/plants-pipeline and is fully implemented in Python and Bash.<\/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\/btab168","type":"journal-article","created":{"date-parts":[[2021,3,8]],"date-time":"2021-03-08T07:13:36Z","timestamp":1615187616000},"page":"3053-3055","source":"Crossref","is-referenced-by-count":7,"title":["LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life"],"prefix":"10.1093","volume":"37","author":[{"given":"William","family":"Goh","sequence":"first","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University , 637551 Singapore, Singapore"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7848-0126","authenticated-orcid":false,"given":"Marek","family":"Mutwil","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University , 637551 Singapore, Singapore"}]}],"member":"286","published-online":{"date-parts":[[2021,3,11]]},"reference":[{"key":"2023061310553399800_btab168-B1","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. 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