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SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data

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Detalles Bibliográficos
Autores principales:	Goepp, Vivien, Saldanha, Oliver Lester, Pfeiffer, Kevin, Kramann, Rafael, Kather, Jakob Nikolas, Hayat, Sikander
Formato:	Recurso digital
Lenguaje:	inglés
Publicado:	Zenodo 2025
Materias:	Single cell Single cell atlas Cell type annotation Swarm learning Classification
Acceso en línea:	Acceder al recurso
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_version_	1866901562270416896
author	Goepp, Vivien Saldanha, Oliver Lester Pfeiffer, Kevin Kramann, Rafael Kather, Jakob Nikolas Hayat, Sikander
author_facet	Goepp, Vivien Saldanha, Oliver Lester Pfeiffer, Kevin Kramann, Rafael Kather, Jakob Nikolas Hayat, Sikander
contents	<p>Data repository for the manuscript Saldanha, Goepp, et al, 2025 "SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data".</p> <p>Contains all the processed data used in the manuscript, which consists of the following, publically available, raw datasets:</p> <p> </p> <table style="border-collapse: collapse; width: 100.063%; height: 949.4px;"><colgroup><col style="width: 6.75393%;"><col style="width: 17.0462%;"><col style="width: 15.2313%;"><col style="width: 12.9581%;"><col style="width: 31.178%;"><col style="width: 6.04712%;"><col style="width: 5.18325%;"><col style="width: 5.73298%;"></colgroup> <tbody> <tr style="height: 58.8px;"> <td style="height: 58.8px;"><br>Collection  </td> <td style="height: 58.8px;">Collection reference</td> <td style="height: 58.8px;">Suspension type</td> <td style="height: 58.8px;">Study reference</td> <td style="height: 58.8px;">Download link</td> <td style="height: 58.8px;">Number of cells</td> <td style="height: 58.8px;">Number of cell types</td> <td style="height: 58.8px;">Number of cell subtypes</td> </tr> <tr style="height: 81.2px;"> <td style="height: 81.2px;"> <p>Heart</p> <p> </p> </td> <td style="height: 81.2px;"><a href="https://www.medrxiv.org/content/early/2025/10/13/2025.10.09.25337646.full.pdf">Bleckwehl et al., 2025</a></td> <td style="height: 81.2px;">single nuclei</td> <td style="height: 81.2px;"><a href="https://doi.org/10.1038/s41586-022-04817-8">Chaffin et al., 2022</a></td> <td style="height: 81.2px;"><a href="https://singlecell.broadinstitute.org/single_cell/study/SCP1303/">Chaffin 2022, Singel Cell Portal</a></td> <td style="height: 81.2px;">560696 (542216)</td> <td style="height: 81.2px;">14</td> <td style="height: 81.2px;">21</td> </tr> <tr style="height: 39.2px;"> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"><a href="https://doi.org/10.1038/s41586-022-05060-x">Kuppe et al., 2022</a></td> <td style="height: 39.2px;"><a href="https://cellxgene.cziscience.com/collections/8191c283-0816-424b-9b61-c3e1d6258a77">Kuppe 2022, CellxGene</a></td> <td style="height: 39.2px;">189349 (146325)</td> <td style="height: 39.2px;">13</td> <td style="height: 39.2px;">21</td> </tr> <tr style="height: 39.2px;"> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"><a href="https://doi.org/10.1038/s41586-020-2797-4">Litvinukova et al., 2020</a></td> <td style="height: 39.2px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e72v">Litvinukova 2020, CellxGene</a></td> <td style="height: 39.2px;">84953 (79916)</td> <td style="height: 39.2px;">14</td> <td style="height: 39.2px;">21</td> </tr> <tr style="height: 39.2px;"> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"><a href="https://doi.org/10.1126/science.abo1984">Reichart et al., 2022</a></td> <td style="height: 39.2px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e72e75342a8-0f3b-4ec5-8ee1-245a23e0f7cb">Reichart 2022, CellxGene</a></td> <td style="height: 39.2px;">361649 (349045)</td> <td style="height: 39.2px;">14</td> <td style="height: 39.2px;">21</td> </tr> <tr style="height: 58.8px;"> <td style="height: 58.8px;">Lung</td> <td style="height: 58.8px;"><a href="https://doi.org/10.1038/s41591-023-02327-2">Sikkema et al., 2023</a></td> <td style="height: 58.8px;">single cell</td> <td style="height: 58.8px;"><a href="https://doi.org/10.1126/sciadv.aba1972">Habermann et al., 2020</a></td> <td style="height: 58.8px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 58.8px;">115249</td> <td style="height: 58.8px;">17</td> <td style="height: 58.8px;">24</td> </tr> <tr style="height: 45px;"> <td style="height: 45px;"> </td> <td style="height: 45px;"> </td> <td style="height: 45px;"> </td> <td style="height: 45px;"><a href="https://doi.org/10.1038/s41586-020-2922-4">Travaglini et al., 2020</a></td> <td style="height: 45px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 45px;">39901</td> <td style="height: 45px;">17</td> <td style="height: 45px;">24</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41586-020-03148-w">Grant et al., 2021</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 98px;">47301</td> <td style="height: 98px;">17</td> <td style="height: 98px;">24</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1164/rccm.201806-1037ED">Misharin & Budinger, 2018</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 98px;">40580</td> <td style="height: 98px;">17</td> <td style="height: 98px;">24</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;">Breast</td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41588-024-01688-9">Reed et al., 2024</a></td> <td style="height: 98px;">single cell </td> <td style="height: 98px;"><a href="https://doi.org/10.1016/j.cels.2022.06.005">Murrow et al., 2022</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">80726</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41588-023-01298-x">Nee et al., 2023</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">219239</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.15252/embj.2020107333">Pal et al., 2021</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">116432</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41467-021-27895-0">Twigger et al., 2022</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">100168</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> </tbody> </table> <p> </p>
format	Recurso digital
id	zenodo_https___doi_org_10_5281_zenodo_17747500
institution	Zenodo
language	eng
publishDate	2025
publisher	Zenodo
record_format	zenodo
spellingShingle	SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data Goepp, Vivien Saldanha, Oliver Lester Pfeiffer, Kevin Kramann, Rafael Kather, Jakob Nikolas Hayat, Sikander Single cell Single cell atlas Cell type annotation Swarm learning Classification <p>Data repository for the manuscript Saldanha, Goepp, et al, 2025 "SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data".</p> <p>Contains all the processed data used in the manuscript, which consists of the following, publically available, raw datasets:</p> <p> </p> <table style="border-collapse: collapse; width: 100.063%; height: 949.4px;"><colgroup><col style="width: 6.75393%;"><col style="width: 17.0462%;"><col style="width: 15.2313%;"><col style="width: 12.9581%;"><col style="width: 31.178%;"><col style="width: 6.04712%;"><col style="width: 5.18325%;"><col style="width: 5.73298%;"></colgroup> <tbody> <tr style="height: 58.8px;"> <td style="height: 58.8px;"><br>Collection  </td> <td style="height: 58.8px;">Collection reference</td> <td style="height: 58.8px;">Suspension type</td> <td style="height: 58.8px;">Study reference</td> <td style="height: 58.8px;">Download link</td> <td style="height: 58.8px;">Number of cells</td> <td style="height: 58.8px;">Number of cell types</td> <td style="height: 58.8px;">Number of cell subtypes</td> </tr> <tr style="height: 81.2px;"> <td style="height: 81.2px;"> <p>Heart</p> <p> </p> </td> <td style="height: 81.2px;"><a href="https://www.medrxiv.org/content/early/2025/10/13/2025.10.09.25337646.full.pdf">Bleckwehl et al., 2025</a></td> <td style="height: 81.2px;">single nuclei</td> <td style="height: 81.2px;"><a href="https://doi.org/10.1038/s41586-022-04817-8">Chaffin et al., 2022</a></td> <td style="height: 81.2px;"><a href="https://singlecell.broadinstitute.org/single_cell/study/SCP1303/">Chaffin 2022, Singel Cell Portal</a></td> <td style="height: 81.2px;">560696 (542216)</td> <td style="height: 81.2px;">14</td> <td style="height: 81.2px;">21</td> </tr> <tr style="height: 39.2px;"> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"><a href="https://doi.org/10.1038/s41586-022-05060-x">Kuppe et al., 2022</a></td> <td style="height: 39.2px;"><a href="https://cellxgene.cziscience.com/collections/8191c283-0816-424b-9b61-c3e1d6258a77">Kuppe 2022, CellxGene</a></td> <td style="height: 39.2px;">189349 (146325)</td> <td style="height: 39.2px;">13</td> <td style="height: 39.2px;">21</td> </tr> <tr style="height: 39.2px;"> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"><a href="https://doi.org/10.1038/s41586-020-2797-4">Litvinukova et al., 2020</a></td> <td style="height: 39.2px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e72v">Litvinukova 2020, CellxGene</a></td> <td style="height: 39.2px;">84953 (79916)</td> <td style="height: 39.2px;">14</td> <td style="height: 39.2px;">21</td> </tr> <tr style="height: 39.2px;"> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"> </td> <td style="height: 39.2px;"><a href="https://doi.org/10.1126/science.abo1984">Reichart et al., 2022</a></td> <td style="height: 39.2px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e72e75342a8-0f3b-4ec5-8ee1-245a23e0f7cb">Reichart 2022, CellxGene</a></td> <td style="height: 39.2px;">361649 (349045)</td> <td style="height: 39.2px;">14</td> <td style="height: 39.2px;">21</td> </tr> <tr style="height: 58.8px;"> <td style="height: 58.8px;">Lung</td> <td style="height: 58.8px;"><a href="https://doi.org/10.1038/s41591-023-02327-2">Sikkema et al., 2023</a></td> <td style="height: 58.8px;">single cell</td> <td style="height: 58.8px;"><a href="https://doi.org/10.1126/sciadv.aba1972">Habermann et al., 2020</a></td> <td style="height: 58.8px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 58.8px;">115249</td> <td style="height: 58.8px;">17</td> <td style="height: 58.8px;">24</td> </tr> <tr style="height: 45px;"> <td style="height: 45px;"> </td> <td style="height: 45px;"> </td> <td style="height: 45px;"> </td> <td style="height: 45px;"><a href="https://doi.org/10.1038/s41586-020-2922-4">Travaglini et al., 2020</a></td> <td style="height: 45px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 45px;">39901</td> <td style="height: 45px;">17</td> <td style="height: 45px;">24</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41586-020-03148-w">Grant et al., 2021</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 98px;">47301</td> <td style="height: 98px;">17</td> <td style="height: 98px;">24</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1164/rccm.201806-1037ED">Misharin & Budinger, 2018</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e726f6d381a-7701-4781-935c-db10d30de293">All Lung Studies</a></td> <td style="height: 98px;">40580</td> <td style="height: 98px;">17</td> <td style="height: 98px;">24</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;">Breast</td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41588-024-01688-9">Reed et al., 2024</a></td> <td style="height: 98px;">single cell </td> <td style="height: 98px;"><a href="https://doi.org/10.1016/j.cels.2022.06.005">Murrow et al., 2022</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">80726</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41588-023-01298-x">Nee et al., 2023</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">219239</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.15252/embj.2020107333">Pal et al., 2021</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">116432</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> <tr style="height: 98px;"> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"> </td> <td style="height: 98px;"><a href="https://doi.org/10.1038/s41467-021-27895-0">Twigger et al., 2022</a></td> <td style="height: 98px;"><a href="https://cellxgene.cziscience.com/collections/b52eb423-5d0d-4645-b217-e1c6d38b2e7248259aa8-f168-4bf5-b797-af8e88da6637">All Breast Studies</a></td> <td style="height: 98px;">100168</td> <td style="height: 98px;">14</td> <td style="height: 98px;">22</td> </tr> </tbody> </table> <p> </p>
title	SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data
topic	Single cell Single cell atlas Cell type annotation Swarm learning Classification
url	https://doi.org/10.5281/zenodo.17747500