{"id":42586,"date":"2026-09-13T14:27:14","date_gmt":"2026-09-13T12:27:14","guid":{"rendered":"https:\/\/www.graviton.at\/letterswaplibrary\/12-compact-traceable-bulk-rna-seq-datasets-derived-from-expression-atlas\/"},"modified":"2026-09-13T14:27:14","modified_gmt":"2026-09-13T12:27:14","slug":"12-compact-traceable-bulk-rna-seq-datasets-derived-from-expression-atlas","status":"publish","type":"post","link":"https:\/\/www.graviton.at\/letterswaplibrary\/12-compact-traceable-bulk-rna-seq-datasets-derived-from-expression-atlas\/","title":{"rendered":"12 Compact, Traceable Bulk RNA-seq Datasets Derived From Expression Atlas"},"content":{"rendered":"<p><!-- SC_OFF --><\/p>\n<div class=\"md\">\n<p>Sharing a dataset collection I&#8217;ve been putting together.<\/p>\n<p><a href=\"https:\/\/github.com\/vxxqv\/openomicsbench\">OpenOmicsBench<\/a> v1 has 12 bulk RNA-seq benchmark datasets derived from seven Expression Atlas studies across human, mouse and Arabidopsis.<\/p>\n<p>Each contains counts, sample metadata, the experimental design, source\/provenance information and a compact version intended for examples or software testing. I also keep validation results against the corresponding full matrix rather than assuming the smaller matrix preserves the original behaviour.<\/p>\n<p>Everything is openly available and versioned, and the collection can either be installed from PyPI or obtained through GitHub\/Zenodo.<\/p>\n<p>I&#8217;d be interested in suggestions for other public RNA-seq study designs worth representing in future versions.<\/p>\n<p>GitHub: <a href=\"https:\/\/github.com\/vxxqv\/openomicsbench\">https:\/\/github.com\/vxxqv\/openomicsbench<\/a><\/p>\n<p>PyPI: <a href=\"https:\/\/pypi.org\/project\/openomicsbench\/\">https:\/\/pypi.org\/project\/openomicsbench\/<\/a><\/p>\n<p>Zenodo: <a href=\"https:\/\/doi.org\/10.5281\/zenodo.22679414\">https:\/\/doi.org\/10.5281\/zenodo.22679414<\/a><\/p>\n<\/div>\n<p><!-- SC_ON -->   submitted by   <a href=\"https:\/\/www.reddit.com\/user\/vxxqv\"> \/u\/vxxqv <\/a> <br \/> <span><a href=\"https:\/\/www.reddit.com\/r\/datasets\/comments\/1wf5mxv\/12_compact_traceable_bulk_rnaseq_datasets_derived\/\">[link]<\/a><\/span>   <span><a href=\"https:\/\/www.reddit.com\/r\/datasets\/comments\/1wf5mxv\/12_compact_traceable_bulk_rnaseq_datasets_derived\/\">[comments]<\/a><\/span><\/p><div class='watch-action'><div class='watch-position align-right'><div class='action-like'><a class='lbg-style1 like-42586 jlk' href='javascript:void(0)' data-task='like' data-post_id='42586' data-nonce='b9a40cecc8' rel='nofollow'><img class='wti-pixel' src='https:\/\/www.graviton.at\/letterswaplibrary\/wp-content\/plugins\/wti-like-post\/images\/pixel.gif' title='Like' \/><span class='lc-42586 lc'>0<\/span><\/a><\/div><\/div> <div class='status-42586 status align-right'><\/div><\/div><div class='wti-clear'><\/div>","protected":false},"excerpt":{"rendered":"<p>Sharing a dataset collection I&#8217;ve been putting together. OpenOmicsBench v1 has 12 bulk RNA-seq benchmark datasets derived&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[85],"tags":[],"class_list":["post-42586","post","type-post","status-publish","format-standard","hentry","category-datatards","wpcat-85-id"],"_links":{"self":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/posts\/42586","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/comments?post=42586"}],"version-history":[{"count":0,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/posts\/42586\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/media?parent=42586"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/categories?post=42586"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.graviton.at\/letterswaplibrary\/wp-json\/wp\/v2\/tags?post=42586"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}