{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:48:01Z","timestamp":1790862481203,"version":"4.1.0"},"posted":{"date-parts":[[2025,1,31]]},"group-title":"Bioinformatics","reference-count":33,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T00:00:00Z","timestamp":1738281600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Changes in cell type composition play an important role in human health and disease. Recent advances in single-cell technology have enabled the measurement of cell type composition at increasing cell lineage resolution across large cohorts of individuals. Yet this raises new challenges for statistical analysis of these compositional data to identify changes in cell type frequency. We introduce\n                  <jats:monospace>crumblr<\/jats:monospace>\n                  (\n                  <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/diseaseneurogenomics.github.io\/crumblr\">DiseaseNeurogenomics.github.io\/crumblr<\/jats:ext-link>\n                  ), a scalable statistical method for analyzing count ratio data using precision-weighted linear mixed models incorporating random effects for complex study designs. Uniquely,\n                  <jats:monospace>crumblr<\/jats:monospace>\n                  performs statistical testing at multiple levels of the cell lineage hierarchy using a multivariate approach to increase power over tests of one cell type. In simulations,\n                  <jats:monospace>crumblr<\/jats:monospace>\n                  increases power compared to existing methods while controlling the false positive rate. We demonstrate the application of\n                  <jats:monospace>crumblr<\/jats:monospace>\n                  to published single-cell RNA-seq datasets for aging, tuberculosis infection in T cells, bone metastases from prostate cancer, and SARS-CoV-2 infection.\n                <\/jats:p>","DOI":"10.1101\/2025.01.29.635498","type":"posted-content","created":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T06:50:34Z","timestamp":1738306234000},"source":"Crossref","is-referenced-by-count":10,"title":["Fast, flexible analysis of differences in cellular composition with crumblr"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0957-0224","authenticated-orcid":false,"given":"Gabriel E.","family":"Hoffman","sequence":"first","affiliation":[{"name":"Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4640-6239","authenticated-orcid":false,"given":"Panos","family":"Roussos","sequence":"additional","affiliation":[{"name":"Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041023255351000_2025.01.29.635498v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.06.031"},{"key":"2026041023255351000_2025.01.29.635498v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-02104-7"},{"key":"2026041023255351000_2025.01.29.635498v1.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.adi5199"},{"key":"2026041023255351000_2025.01.29.635498v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08338-4"},{"key":"2026041023255351000_2025.01.29.635498v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-023-01421-y"},{"key":"2026041023255351000_2025.01.29.635498v1.6","doi-asserted-by":"publisher","DOI":"10.1126\/science.adf1226"},{"key":"2026041023255351000_2025.01.29.635498v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2023.10.013"},{"key":"2026041023255351000_2025.01.29.635498v1.8","doi-asserted-by":"publisher","DOI":"10.1101\/2024.10.31.24316513"},{"key":"2026041023255351000_2025.01.29.635498v1.9","doi-asserted-by":"publisher","DOI":"10.1101\/2024.11.06.24316592"},{"key":"2026041023255351000_2025.01.29.635498v1.10","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-2-r29"},{"key":"2026041023255351000_2025.01.29.635498v1.11","doi-asserted-by":"crossref","unstructured":"Love, M. 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