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1<path d="M22.7 11.006c-4.619-.13-8.981 1.991-11.54 5.612-.76 1.122 1.399 2.113 2.158.995 1.924-2.846 5.602-4.652 9.569-4.557 4.072.132 7.804 2.17 9.948 5.431.76 1.181 2.755.109 1.995-1.064-2.418-3.756-7.15-6.313-12.13-6.417Z" fill="url(#c)"></path><path fill-rule="evenodd" clip-rule="evenodd" d="M7.708 5.359a21.784 21.784 0 0 1 30.176 1.5c7.403 7.815 8.207 19.895 1.905 28.648L55.7 52.3a1.093 1.093 0 0 1-.029 1.538l-3.963 3.856a1.06 1.06 0 0 1-1.516-.028l-15.91-16.793c-9.68 6.595-22.75 4.385-29.8-5.037-7.051-9.423-5.636-22.79 3.227-30.477Zm2.96 28.054a15.584 15.584 0 0 0 22.26.445v-.005c6.266-6.114 6.462-16.224.436-22.583a15.584 15.584 0 0 0-22.259-.441c-6.267 6.114-6.463 16.225-.437 22.584Z" fill="#386DB0"></path><path d="M11.5 18c-2 0-2 3 0 3s2-3 0-3ZM22.7 10.006c-4.619-.13-8.981 1.991-11.54 5.612-.76 1.122 1.399 2.113 2.158.995 1.924-2.846 5.602-4.652 9.569-4.557 4.072.132 7.804 2.17 9.948 5.431.76 1.181 2.755.109 1.995-1.064-2.418-3.756-7.15-6.313-12.13-6.417Z" fill="#386DB0"></path><defs><linearGradient id="a" x1="56.016" y1="60.984" x2="56.016" y2="2.989" gradientUnits="userSpaceOnUse"><stop stop-color="#B3B3B3" stop-opacity=".25"></stop><stop offset=".54" stop-color="#B3B3B3" stop-opacity=".1"></stop><stop offset="1" stop-color="#B3B3B3" stop-opacity=".05"></stop></linearGradient><linearGradient id="b" x1="13" y1="24" x2="13" y2="21" gradientUnits="userSpaceOnUse"><stop stop-opacity=".12"></stop><stop offset=".55" stop-opacity=".09"></stop><stop offset="1" stop-opacity=".02"></stop></linearGradient><linearGradient id="c" x1="35.014" y1="19.012" x2="35.014" y2="11.001" gradientUnits="userSpaceOnUse"><stop stop-opacity=".12"></stop><stop offset=".55" stop-opacity=".09"></stop><stop offset="1" stop-opacity=".02"></stop></linearGradient></defs></svg></div><div class="StyledBox-sc-13pk1d4-0 bpcrKd"><h2 class="StyledHeading-sc-1rdh4aw-0 bXkChf">Find the data you need</h2><p class="StyledParagraph-sc-tbetod-0 cvIxYO">Search the multi-organism collection of genome wide gene expression data obtained from publicly available sources like GEO, ArrayExpress, and SRA. The data has been processed uniformly and normalized using a set of<!-- --> <a target="_blank" rel="noopener noreferrer" class="StyledAnchor-sc-1rp7lwl-0 cKcXuX Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="https://docs.refine.bio/en/latest/main_text.html#processing-information">standardized pipelines</a> <!-- -->curated by the<!-- --> <a target="_blank" rel="noopener noreferrer" class="StyledAnchor-sc-1rp7lwl-0 cKcXuX Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="https://www.ccdatalab.org">Childhood Cancer Data Lab (CCDL)</a></p></div></div></div><div class="StyledBox-sc-13pk1d4-0 egQqUu"><div class="StyledBox-sc-13pk1d4-0 fQMCWK"><div aria-hidden="true" class="StyledBox-sc-13pk1d4-0 eOlLus"><svg width="69" height="59" fill="none" xmlns="http://www.w3.org/2000/svg"><path d="M68.052 54.714h-60v-40h7.674l3.157 4.161h49.17v35.839Z" fill="#386DB0"></path><path opacity=".1" d="M68.052 54.714h-60v-40h7.674l3.157 4.161h49.17v35.839Z" fill="#000"></path><path d="M22.16 10.125 49.904 0l16.58 46.246L38.74 56.371 22.16 10.125Z" fill="silver"></path><path d="m29.62 12.94 8.444-3.08.436 1.216-8.444 3.082-.436-1.217ZM31.198 17.251l18.12-6.528.432 1.219-18.121 6.528-.431-1.219ZM32.48 22.428 50.601 15.9l.431 1.219-18.12 6.528-.432-1.22ZM33.763 25.016l18.12-6.528.432 1.22-18.12 6.527-.432-1.219ZM31.198 28.899l18.12-6.528.432 1.219-18.121 6.528-.431-1.22ZM32.48 34.075l18.121-6.528.431 1.22-18.12 6.527-.432-1.219ZM33.763 37.958l18.12-6.528.432 1.219-18.12 6.528-.432-1.22ZM48.277 38.01l3.624-1.305 1.294 3.656-3.624 1.306-1.294-3.657Z" fill="#FDFDFD"></path><path d="M.204 29.291 15.93 2.59l43.007 25.784L43.21 55.075.204 29.291Z" fill="url(#a)"></path><path d="m.441 28.419 15.072-25.59 41.904 25.123-15.072 25.59L.441 28.418Z" fill="silver"></path><path d="m9.409 28.513 4.586-7.788 1.103.662-4.587 7.787-1.102-.66ZM14.484 30.375l9.829-16.688 1.103.66-9.83 16.69-1.102-.662ZM17.05 31.67l9.828-16.69 1.103.662-9.829 16.689-1.103-.662ZM19.622 34.263l9.814-16.697 1.104.66-9.815 16.697-1.103-.66ZM24.746 35.552l9.829-16.689 1.103.662-9.83 16.688-1.102-.661Z" fill="#FDFDFD"></path><path d="m23.463 39.434 9.83-16.688 1.102.661-9.83 16.689-1.102-.661ZM26.029 40.729l9.829-16.689 1.102.661-9.829 16.689-1.102-.661ZM37.837 29.512l1.963-3.34 3.31 1.981-1.963 3.34-3.31-1.98ZM62.748 26.699l.364-3.865 3.831.367-.364 3.865-3.83-.367Z" fill="#FDFDFD"></path><path d="M68.052 58.714h-60v-40h7.674l3.157 4.162h49.17v35.838Z" fill="#386DB0"></path><path opacity=".1" d="M30.052 37.714h13v3h-13v-3Z" fill="#000"></path><defs><linearGradient id="a" x1="59.141" y1="28.266" x2="15.93" y2="2.588" gradientUnits="userSpaceOnUse"><stop stop-color="gray" stop-opacity=".25"></stop><stop offset=".54" stop-color="gray" stop-opacity=".12"></stop><stop offset="1" stop-color="gray" stop-opacity=".1"></stop></linearGradient></defs></svg></div><div class="StyledBox-sc-13pk1d4-0 bpcrKd"><h2 class="StyledHeading-sc-1rdh4aw-0 bXkChf">Create custom datasets</h2><p class="StyledParagraph-sc-tbetod-0 cvIxYO">Build and download custom datasets tailored to your needs including gene expression matrices and sample metadata.</p></div></div></div></div></div></div><div class="StyledBox-sc-13pk1d4-0 fDXlPn"><div style="position:relative" class="StyledBox-sc-13pk1d4-0 cQCjQj"><div class="StyledBox-sc-13pk1d4-0 hYwaBV"><p class="StyledParagraph-sc-tbetod-0 jkHfAX">You can use refine.bio datasets for preliminary assessment of biological signals and to accelerate validation of your research f
1indings.</p></div><div class="StyledBox-sc-13pk1d4-0 fQMCWK"><div class="StyledBox-sc-13pk1d4-0 bIxJEk"><div aria-hidden="true" class="StyledBox-sc-13pk1d4-0 jXhhWw"><svg width="59" height="57" fill="none" xmlns="http://www.w3.org/2000/svg"><path d="m54.725 27.6 4.075 4.8-4.075 4.8H31.2v-9.6h23.525ZM54.725 13.2 58.8 18l-4.075 4.8H31.2v-9.6h23.525Z" fill="#386DB0"></path><path d="M29.4 0c2.978 0 5.4 2.422 5.4 5.4s-2.422 5.4-5.4 5.4A5.405 5.405 0 0 1 24 5.4C24 2.422 26.422 0 29.4 0Z" fill="#AAC4E4"></path><path d="M4.075 26.4 0 21.6l4.075-4.8H27.6v9.6H4.075ZM4.075 44.4 0 39.6l4.075-4.8H27.6v9.6H4.075Z" fill="#386DB0"></path><path d="M27.368 44.893V9.126c.782.058 1.581.094 2.4.094.818 0 1.617-.036 2.4-.094v43.2l-4.8-.954v-6.479Z" fill="#AAC4E4"></path><path d="m24.6 48 18.6 8.4H6L24.6 48ZM36.656 48 52.8 56.4h-9.513L32.4 51.508 36.656 48Z" fill="#41A36D"></path><path fill="#F2F2F2" d="M23.226 38.477h1.935v1.935h-1.935zM19.355 38.477h1.935v1.935h-1.935zM15.484 38.477h1.935v1.935h-1.935zM22.142 20.4h1.935v1.935h-1.935zM18.271 20.4h1.935v1.935h-1.935zM14.4 20.4h1.935v1.935H14.4zM42.542 16.8h1.935v1.935h-1.935zM38.671 16.8h1.935v1.935h-1.935zM34.8 16.8h1.935v1.935H34.8zM42.542 31.2h1.935v1.935h-1.935zM38.671 31.2h1.935v1.935h-1.935zM34.8 31.2h1.935v1.935H34.8z"></path></svg></div><h4 class="StyledHeading-sc-1rdh4aw-0 bCDDrD">Get Started using refine.bio data</h4><p class="StyledParagraph-sc-tbetod-0 haRUhC">Explore the different ways you can use refine.bio data to help with your scientific questions.</p><div class="StyledBox-sc-13pk1d4-0 ixKOzD"><div style="display:flex" class="StyledBox-sc-13pk1d4-0 kWlcJP"><a rel="noopener noreferrer" target="_blank" class="StyledButtonKind-sc-1vhfpnt-0 cztAvm Button__CustomButton-sc-8ptgho-1 dGJVZV" href="https://alexslemonade.github.io/refinebio-examples/index.html">Get Started</a></div></div></div><div class="StyledBox-sc-13pk1d4-0 fMuIKT"><div aria-hidden="true" class="StyledBox-sc-13pk1d4-0 jXhhWw"><svg width="80" height="47" fill="none" xmlns="http://www.w3.org/2000/svg"><rect width="80" height="47" rx="2" fill="#F2F2F2"></rect><path fill="#386DB0" d="M4 3h32.941v9.75H4z"></path><path fill="#FDFDFD" d="M4 12.75h32.941v9.75H4z"></path><path fill="#80A6D6" d="M4 22.5h32.941v9.75H4z"></path><path fill="#D4E1F1" d="M4 32.25h32.941V42H4z"></path><path fill="#80A6D6" d="M41.059 3H74v9.75H41.059z"></path><path fill="#D4E1F1" d="M41.059 12.75H74v9.75H41.059z"></path><path fill="#FDFDFD" d="M41.059 22.5H74v9.75H41.059z"></path><path fill="#AAC4E4" d="M41.059 32.25H74V42H41.059z"></path></svg></div><h4 class="StyledHeading-sc-1rdh4aw-0 bCDDrD">Differential Expression Analysis</h4><p class="StyledParagraph-sc-tbetod-0 haRUhC">Learn how you can do differential expression analysis with refine.bio datasets.</p><div class="StyledBox-sc-13pk1d4-0 ixKOzD"><div style="display:flex" class="StyledBox-sc-13pk1d4-0 kWlcJP"><a rel="noopener noreferrer" target="_blank" class="StyledButtonKind-sc-1vhfpnt-0 cztAvm Button__CustomButton-sc-8ptgho-1 dGJVZV" href="https://alexslemonade.github.io/refinebio-examples/03-rnaseq/differential-expression_rnaseq_01.html">RNA-seq Example</a></div><div style="display:flex" class="StyledBox-sc-13pk1d4-0 kWlcJP"><a rel="noopener noreferrer" target="_blank" class="StyledButtonKind-sc-1vhfpnt-0 gGngUK Button__CustomButton-sc-8ptgho-1 dGJVZV" href="https://alexslemonade.github.io/refinebio-examples/02-microarray/differential-expression_microarray_01_2-groups.html">Microarray Example</a></div></div></div><div class="StyledBox-sc-13pk1d4-0 qemYk"><div aria-hidden="true" class="StyledBox-sc-13pk1d4-0 jXhhWw"><svg width="56" height="55" fill="none" xmlns="http://www.w3.org/2000/svg"><path fill-rule="evenodd" clip-rule="evenodd" d="m9.537 9.897 3.5-2.383s13.259 11.171 18.867 17.351C37.513 31.045 46.47 43.24 46.47 43.24l-3.265 2.934s-8.102-13.59-13.774-20.01C23.758 19.747 9.537 9.898 9.537 9.898Z" fill="#41A36D"></path><path fill-rule="evenodd" clip-rule="evenodd" d="m39.87 5.131 3.268 2.619s-6.196 13.08-11.75 19.908c-5.553 6.829-16.184 21.516-16.184 21.516l-3.334-3.532s11.778-12.535 17.56-19.477c5.782-6.942 10.44-21.034 10.44-21.034Z" fill="#386DB0"></path><path fill-rule="evenodd" clip-rule="evenodd" d="M3.704 28.961s17.648-2.28 21.819.688c4.17 2.969 4.68 22.525 4.68 22.525l-5.5-.626s2.957-16.986-1.148-19.908c-4.105-2.922-19.851 1.534-19.851 1.534V28.96Z" fill="#AAC4E4"></path><path fill-rule="evenodd" clip-rule="evenodd" d="M51.945 23.384s-16.813 2.572-21.083-.247c-4.27-2.82-4.956-21.022-4.956-21.022h4.63s-1.979
116.188 2.224 18.962c4.203 2.775 18.04-2.224 18.04-2.224l1.145 4.531Z" fill="#41A36D"></path><path fill-rule="evenodd" clip-rule="evenodd" d="m6.204 15.174 3.37-4s16.254 7.97 16.621 15.096c.368 7.126-15.991 18.904-15.991 18.904l-2.278-3.357s15.732-8.903 15.732-14.052c0-5.15-17.454-12.591-17.454-12.591Z" fill="#80A6D6"></path><path fill-rule="evenodd" clip-rule="evenodd" d="m43.628 7.75 3.184 2.986s-9.775 9.788-11.507 17.17c-1.732 7.384 2.448 22.149 2.448 22.149l-4.406.995s-2.653-17.94-.49-25.383C35.02 18.225 43.628 7.75 43.628 7.75Z" fill="#AAC4E4"></path><ellipse cx="27.704" cy="27.174" rx="24.5" ry="25" stroke="#386DB0"></ellipse></svg></div><h4 class="StyledHeading-sc-1rdh4aw-0 bCDDrD">Pathway Analysis</h4><p class="StyledParagraph-sc-tbetod-0 haRUhC">Learn how you can use refine.bio data to identify pathways that are active in your biological condition of interest.</p><div class="StyledBox-sc-13pk1d4-0 ixKOzD"><div style="display:flex" class="StyledBox-sc-13pk1d4-0 kWlcJP"><a rel="noopener noreferrer" target="_blank" class="StyledButtonKind-sc-1vhfpnt-0 cztAvm Button__CustomButton-sc-8ptgho-1 dGJVZV" href="https://alexslemonade.github.io/refinebio-examples/03-rnaseq/pathway-analysis_rnaseq_02_gsea.html">RNA-seq Example</a></div><div style="display:flex" class="StyledBox-sc-13pk1d4-0 kWlcJP"><a rel="noopener noreferrer" target="_blank" class="StyledButtonKind-sc-1vhfpnt-0 gGngUK Button__CustomButton-sc-8ptgho-1 dGJVZV" href="https://alexslemonade.github.io/refinebio-examples/02-microarray/pathway-analysis_microarray_02_gsea.html">Microarray Example</a></div></div></div></div></div></div><div class="StyledBox-sc-13pk1d4-0 hFNraN"><div style="position:relative" class="StyledBox-sc-13pk1d4-0 cQCjQj"><div class="StyledBox-sc-13pk1d4-0 fQMCWK"><div class="StyledBox-sc-13pk1d4-0 hzalnX"><h1 class="StyledHeading-sc-1rdh4aw-0 fxMKJL">refine.bio Compendia</h1><p class="StyledParagraph-sc-tbetod-0 haRUhC">refine.bio compendia are collections of samples that have been 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Greene, Dongbo Hu<!-- -->, <!-- --> <!-- -->Richard W. W. Jones<!-- -->, <!-- --> <!-- -->Stephanie Liu<!-- -->, <!-- --> <!-- -->David S. Mejia<!-- -->, <!-- --> <!-- -->Rob Patro<!-- -->, <!-- --> <!-- -->Stephen R. Piccolo<!-- -->, <!-- --> <!-- -->Ariel Rodriguez Romero<!-- -->, <!-- --> <!-- -->Hirak Sarkar<!-- -->, <!-- --> <!-- -->Candace L. Savonen<!-- -->, <!-- --> <!-- -->Jaclyn N. Taroni<!-- -->, <!-- --> <!-- -->William E. Vauclain<!-- -->, <!-- --> <!-- -->Deepashree Venkatesh Prasad<!-- -->, <!-- --> <!-- -->Kurt G. Wheeler<!-- -->, <!-- --> <!-- -->Arkadii Yakovets<!-- -->, <!-- --> <!-- -->Nozomi Ichihara<!-- -->.<!-- --> <strong>refine.bio: a resource of uniformly processed publicly available gene expression datasets.</strong></span><span class="StyledText-sc-1sadyjn-0 kixbWF">URL:<!-- --> <a target="_blank" rel="nofollow" class="StyledAnchor-sc-1rp7lwl-0 ijUisb Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="https://www.refine.bio">https://www.refine.bio</a></span>
1<p class="StyledParagraph-sc-tbetod-0 heOyEn"><i>Note that the contributor list is in alphabetical order as we prepare a manuscript for submission</i></p></div></div></div><div class="StyledBox-sc-13pk1d4-0 gvWrBN"><div class="StyledBox-sc-13pk1d4-0 fQMCWK"><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="/license">BDS 3-Clause License</a><div class="StyledBox__StyledBoxGap-sc-13pk1d4-1 hbAHdy"></div><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="/privacy">Privacy</a><div class="StyledBox__StyledBoxGap-sc-13pk1d4-1 hbAHdy"></div><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="/terms">Terms of Use</a><div class="StyledBox__StyledBoxGap-sc-13pk1d4-1 hbAHdy"></div><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="mailto:[email protected]">Contact</a></div><div class="StyledBox-sc-13pk1d4-0 faiElH"><span class="StyledText-sc-1sadyjn-0 jsgMtg">Version <!-- -->1.46.22<!-- --> - <!-- -->.0.0</span></div></div></div></footer><div style="bottom:5vh;display:none;position:fixed;right:5vw;z-index:4" class="StyledBox-sc-13pk1d4-0 gyhkwO"><div tabindex="0" role="button" style="box-shadow:none" class="StyledBox-sc-13pk1d4-0 fDSRyR"><div style="position:relative;transform:rotate(-45deg)" class="StyledBox-sc-13pk1d4-0 lbAbcj BackToTopButton__ArrowIcon-sc-bourn0-0 hCljmS"></div><span class="StyledText-sc-1sadyjn-0 irCqcv"><strong>Back to Top</strong></span></div></div><div id="portal" class="StyledBox-sc-13pk1d4-0 bjWreY"></div></div></div></div>
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