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</a><a class="btn btn-light btn-outline-dark btn-discourse" href=https://discourse.scverse.org target=_blank>Discourse</a>
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</a><a class="btn btn-light btn-outline-dark btn-youtube" href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></div></div><div class=col-6><div id=cover-image class="d-none d-lg-block"><img src=img/cover_pca.svg class=w-100></div></div></div><section id=packages><div class=section-heading>Core packages</div><div class=section-content><div class=row id=packages-list><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=anndata-tile><div class="package-icon my-4"><img src=img/icons/anndata.svg></div><div class="card-body package-text p-2"><a href=https://anndata.readthedocs.io/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">anndata</h5><p class="card-text package-desc">Standard for annotated matrices</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=mudata-tile><div class="package-icon my-4"><img src=img/icons/mudata.svg></div><div class="card-body package-text p-2"><a href=https://mudata.readthedocs.io/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">mudata</h5><p class="card-text package-desc">Multimodal data format</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=scanpy-tile><div class="package-icon my-4"><img src=img/icons/scanpy.svg></div><div class="card-body package-text p-2"><a href=https://scanpy.readthedocs.io/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">scanpy</h5><p class="card-text package-desc">Single-cell analysis framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=muon-tile><div class="package-icon my-4"><img src=img/icons/muon.svg></div><div class="card-body package-text p-2"><a href=https://muon.scverse.org/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">muon</h5><p class="card-text package-desc">Multi-omics analysis framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=scvi-tools-tile><div class="package-icon my-4"><img src=img/icons/scvi-tools.svg></div><div class="card-body package-text p-2"><a href=https://scvi-tools.org/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">scvi-tools</h5><p class="card-text package-desc">Single-cell machine learning framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=scirpy-tile><div class="package-icon my-4"><img src=img/icons/scirpy.svg></div><div class="card-body package-text p-2"><a href=https://icbi-lab.github.io/scirpy/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">scirpy</h5><p class="card-text package-desc">Single-cell immune sequencing analysis framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=squidpy-tile><div class="package-icon my-4"><img src=img/icons/squidpy.svg></div><div class="card-body package-text p-2"><a href=https://squidpy.readthedocs.io/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">squidpy</h5><p class="card-text package-desc">Spatial single cell analysis</p></div></div></div></div><a href=/packages><div class=more>View all scverse packages</div></a></div></section><section id=ecosystem><div class=section-heading>Ecosystem</div><div class=section-content><p class=section-paragraph>A broader ecosystem of packages builds on the <strong>scverse</strong> core packages. <a href=/packages/#ecosystem>These tools</a> implement models and analytical approaches to tackle challenges in spatial omics, regulatory genomics, trajectory inference, visualization, and more.</p><a href=/packages/#ecosystem><div class=more>Continue to scverse ecosystem</div></a></div></section><section id=mission><div class=section-heading>Mission</div><div class=section-content><p class=section-paragraph><strong>scverse</strong> is a consortium of foundational tools (mostly in Python) for omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.</p><a href=/about><div class=more>Read more about scverse</div></a></div></section><section id=team><div class=section-heading>Team</div><div class=section-content><p class=section-paragraph><strong>scverse</strong> is a community project currently governed by the developers of the core packages. Please <a href=/join>reach out</a> if you&rsquo;d like to be involved!</p><a href=/people><div class=more>Learn more about scverse community</div></a></div></section><section id=references><div class=section-heading>References</div><div class=section-content><p class=section-paragraph><strong>scverse</strong> tools are used in numerous research and industry projects across the globe and are referenced in <a href="https://scholar.google.ru/scholar?cites=14568046068402025757">thousands</a> of academic publications. Consider consulting the following references for more information about core <strong>scverse</strong> libraries and citing the relevant articles when using them in your work:</p><div class=tiles-list id=refs-list><a href=https://www.nature.com/articles/s41587-023-01733-8 target=_blank><div class=ref-tile id=scverse-ref-tile><div class=ref-text>Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M, scverse community, Berger B, Pe'er D, Regev A, Teichmann S, Finotello F, Wolf F, Yosef N, Stegle O, Theis F: The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology. 2023 April 10</div></div></a><a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0 target=_blank><div class=ref-tile id=scanpy-ref-tile><div class=ref-text>Wolf F, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology 19, 15 (2018)</div></div></a><a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02577-8 target=_blank><div class=ref-tile id=muon-ref-tile><div class=ref-text>Bredikhin D, Kats I, Stegle O. MUON: multimodal omics analysis framework. Genome Biology 23, 42 (2022)</div></div></a><a href=https://www.biorxiv.org/content/10.1101/2021.12.16.473007 target=_blank><div class=ref-tile id=anndata-ref-tile><div class=ref-text>Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. anndata: Annotated data. bioRxiv. 2021 Dec 19.</div></div></a><a href=https://www.nature.com/articles/s41587-021-01206-w target=_blank><div class=ref-tile id=scvi-tools-ref-tile><div class=ref-text>Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y. A Python library for probabilistic analysis of single-cell omics data. Nature Biotechnology. 2022 Feb 7:1-4.</div></div></a><a href=https://academic.oup.com/bioinformatics/article/36/18/4817/5866543 target=_blank><div class=ref-tile id=scirpy-ref-tile><div class=ref-text>Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics. 2020 Sep 15;36(18):4817-8.</div></div></a><a href=https://doi.org/10.1038/s41592-021-01358-2 target=_blank><div class=ref-tile id=Squidpy-ref-tile><div class=ref-text>Palla G, Spitzer H, Klein M, Fischer D, Schaar AC, Kuemmerle LB, Rybakov S, Ibarra IL, Holmberg O, Virshup I, Lotfollahi M, Richter S, Theis FJ. Squidpy: a scalable framework for spatial omics analysis. Nature Methods 19, 171–178 (2022).</div></div></a></div></div></section></div></div></div><footer><div id=footer-content class=container><div class=row><div class="col-12 col-md-6 col-lg-3"><ul><h5>Pages</h5><li><a href=/packages>Packages</a></li><li><a href=/learn>Learn</a></li><li><a href=/people>People</a></li><li><a href=/blog>Blog</a></li><li><a href=/events>Events</a></li><li><a href=/about>About</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><ul><h5>Governance</h5><li><a href=/about/mission/>Mission statement</a></li><li><a href=/about/code_of_conduct>Code of conduct</a></li><li><a href=/about/roles>Roles</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><ul><h5>Join scverse</h5><li><a href=https://github.com/scverse target=_blank>GitHub</a></li><li><a href=https://discourse.scverse.org/ target=_blank>Discourse</a></li><li><a href=https://scverse.zulipchat.com/ target=_blank>Zulip</a></li><li><a href=https://twitter.com/scverse_team target=_blank>Twitter</a></li><li><a href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></li></ul></div></div><div class=signature><p>scverse core team, 2024</p></div></div></footer></body></html>
</a><a class="btn btn-light btn-outline-dark btn-youtube" href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></div></div><div class=col-6><div id=cover-image class="d-none d-lg-block"><img src=img/cover_pca.svg class=w-100></div></div></div><section id=packages><div class=section-heading>Core packages</div><div class=section-content><div class=row id=packages-list><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=anndata-tile><div class="package-icon my-4"><img src=img/icons/anndata.svg></div><div class="card-body package-text p-2"><a href=https://anndata.readthedocs.io/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">anndata</h5><p class="card-text package-desc">Standard for annotated matrices</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=mudata-tile><div class="package-icon my-4"><img src=img/icons/mudata.svg></div><div class="card-body package-text p-2"><a href=https://mudata.readthedocs.io/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">mudata</h5><p class="card-text package-desc">Multimodal data format</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=scanpy-tile><div class="package-icon my-4"><img src=img/icons/scanpy.svg></div><div class="card-body package-text p-2"><a href=https://scanpy.readthedocs.io/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">scanpy</h5><p class="card-text package-desc">Single-cell analysis framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=muon-tile><div class="package-icon my-4"><img src=img/icons/muon.svg></div><div class="card-body package-text p-2"><a href=https://muon.scverse.org/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">muon</h5><p class="card-text package-desc">Multi-omics analysis framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=scvi-tools-tile><div class="package-icon my-4"><img src=img/icons/scvi-tools.svg></div><div class="card-body package-text p-2"><a href=https://scvi-tools.org/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">scvi-tools</h5><p class="card-text package-desc">Single-cell machine learning framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=scirpy-tile><div class="package-icon my-4"><img src=img/icons/scirpy.svg></div><div class="card-body package-text p-2"><a href=https://icbi-lab.github.io/scirpy/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">scirpy</h5><p class="card-text package-desc">Single-cell immune sequencing analysis framework</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=squidpy-tile><div class="package-icon my-4"><img src=img/icons/squidpy.svg></div><div class="card-body package-text p-2"><a href=https://squidpy.readthedocs.io/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">squidpy</h5><p class="card-text package-desc">Spatial single cell analysis</p></div></div></div><div class="col-xs-12 col-sm-12 col-md-12 col-lg-6 py-3"><div class="card border-0 bh-light px-3" id=spatialdata-tile><div class="package-icon my-4"><img src=img/icons/spatialdata.svg></div><div class="card-body package-text p-2"><a href=https://spatialdata.scverse.org/en/latest/ class=stretched-link target=_blank></a><h5 class="card-title mb-1 package-name">spatialdata</h5><p class="card-text package-desc">Spatial data format</p></div></div></div></div><a href=/packages><div class=more>View all scverse packages</div></a></div></section><section id=ecosystem><div class=section-heading>Ecosystem</div><div class=section-content><p class=section-paragraph>A broader ecosystem of packages builds on the <strong>scverse</strong> core packages. <a href=/packages/#ecosystem>These tools</a> implement models and analytical approaches to tackle challenges in spatial omics, regulatory genomics, trajectory inference, visualization, and more.</p><a href=/packages/#ecosystem><div class=more>Continue to scverse ecosystem</div></a></div></section><section id=mission><div class=section-heading>Mission</div><div class=section-content><p class=section-paragraph><strong>scverse</strong> is a consortium of foundational tools (mostly in Python) for omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.</p><a href=/about><div class=more>Read more about scverse</div></a></div></section><section id=team><div class=section-heading>Team</div><div class=section-content><p class=section-paragraph><strong>scverse</strong> is a community project currently governed by the developers of the core packages. Please <a href=/join>reach out</a> if you&rsquo;d like to be involved!</p><a href=/people><div class=more>Learn more about scverse community</div></a></div></section><section id=references><div class=section-heading>References</div><div class=section-content><p class=section-paragraph><strong>scverse</strong> tools are used in numerous research and industry projects across the globe and are referenced in <a href="https://scholar.google.ru/scholar?cites=14568046068402025757">thousands</a> of academic publications. Consider consulting the following references for more information about core <strong>scverse</strong> libraries and citing the relevant articles when using them in your work:</p><div class=tiles-list id=refs-list><a href=https://www.nature.com/articles/s41587-023-01733-8 target=_blank><div class=ref-tile id=scverse-ref-tile><div class=ref-text>Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M, scverse community, Berger B, Pe'er D, Regev A, Teichmann S, Finotello F, Wolf F, Yosef N, Stegle O, Theis F: The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology. 2023 April 10</div></div></a><a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0 target=_blank><div class=ref-tile id=scanpy-ref-tile><div class=ref-text>Wolf F, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology 19, 15 (2018)</div></div></a><a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02577-8 target=_blank><div class=ref-tile id=muon-ref-tile><div class=ref-text>Bredikhin D, Kats I, Stegle O. MUON: multimodal omics analysis framework. Genome Biology 23, 42 (2022)</div></div></a><a href=https://www.biorxiv.org/content/10.1101/2021.12.16.473007 target=_blank><div class=ref-tile id=anndata-ref-tile><div class=ref-text>Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. anndata: Annotated data. bioRxiv. 2021 Dec 19</div></div></a><a href=https://www.nature.com/articles/s41587-021-01206-w target=_blank><div class=ref-tile id=scvi-tools-ref-tile><div class=ref-text>Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y. A Python library for probabilistic analysis of single-cell omics data. Nature Biotechnology. 2022 Feb 7:1-4</div></div></a><a href=https://academic.oup.com/bioinformatics/article/36/18/4817/5866543 target=_blank><div class=ref-tile id=scirpy-ref-tile><div class=ref-text>Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics. 2020 Sep 15;36(18):4817-8</div></div></a><a href=https://doi.org/10.1038/s41592-021-01358-2 target=_blank><div class=ref-tile id=squidpy-ref-tile><div class=ref-text>Palla G, Spitzer H, Klein M, Fischer D, Schaar AC, Kuemmerle LB, Rybakov S, Ibarra IL, Holmberg O, Virshup I, Lotfollahi M, Richter S, Theis FJ. Squidpy: a scalable framework for spatial omics analysis. Nature Methods 19, 171–178 (2022)</div></div></a><a href=https://doi.org/10.1038/s41592-024-02212-x target=_blank><div class=ref-tile id=spatialdata-ref-tile><div class=ref-text>Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B. SpatialData: an open and universal data framework for spatial omics. Nature Methods. 2024 Mar 20:1-5</div></div></a></div></div></section></div></div></div><footer><div id=footer-content class=container><div class=row><div class="col-12 col-md-6 col-lg-3"><ul><h5>Pages</h5><li><a href=/packages>Packages</a></li><li><a href=/learn>Learn</a></li><li><a href=/people>People</a></li><li><a href=/blog>Blog</a></li><li><a href=/events>Events</a></li><li><a href=/about>About</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><ul><h5>Governance</h5><li><a href=/about/mission/>Mission statement</a></li><li><a href=/about/code_of_conduct>Code of conduct</a></li><li><a href=/about/roles>Roles</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><ul><h5>Join scverse</h5><li><a href=https://github.com/scverse target=_blank>GitHub</a></li><li><a href=https://discourse.scverse.org/ target=_blank>Discourse</a></li><li><a href=https://scverse.zulipchat.com/ target=_blank>Zulip</a></li><li><a href=https://twitter.com/scverse_team target=_blank>Twitter</a></li><li><a href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></li></ul></div></div><div class=signature><p>scverse core team, 2024</p></div></div></footer></body></html>
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