{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T12:13:11Z","timestamp":1772021591903,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG002585"],"award-info":[{"award-number":["R01HG002585"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Motivated by theoretical and practical issues that arise when applying Principal component analysis (PCA) to count data, Townes et al. introduced \u201cPoisson GLM-PCA\u201d, a variation of PCA adapted to count data, as a tool for dimensionality reduction of single-cell RNA sequencing (scRNA-seq) data. However, fitting GLM-PCA is computationally challenging. Here we study this problem, and show that a simple algorithm, which we call \u201cAlternating Poisson Regression\u201d (APR), produces better quality fits, and in less time, than existing algorithms. APR is also memory-efficient and lends itself to parallel implementation on multi-core processors, both of which are helpful for handling large scRNA-seq datasets. We illustrate the benefits of this approach in three publicly available scRNA-seq datasets. The new algorithms are implemented in an R package, fastglmpca.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The fastglmpca R package is released on CRAN for Windows, macOS and Linux, and the source code is available at github.com\/stephenslab\/fastglmpca under the open source GPL-3 license. Scripts to reproduce the results in this paper are also available in the GitHub repository and on Zenodo.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae494","type":"journal-article","created":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T23:54:49Z","timestamp":1723074889000},"source":"Crossref","is-referenced-by-count":2,"title":["Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-7809-1649","authenticated-orcid":false,"given":"Eric","family":"Weine","sequence":"first","affiliation":[{"name":"Laboratory for Information and Decision Systems, Massachusetts Institute of Technology , Cambridge, MA 02139, United States"},{"name":"Department of Data Science, Dana Farber Cancer Institute , Boston, MA 02215, United States"}]},{"given":"Peter","family":"Carbonetto","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, University of Chicago , Chicago, IL 60637, United States"}]},{"given":"Matthew","family":"Stephens","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, University of Chicago , Chicago, IL 60637, United States"},{"name":"Department of Statistics, University of Chicago , Chicago, IL 60637, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,8,7]]},"reference":[{"key":"2024081404511934900_btae494-B1","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1093\/bioinformatics\/btac149","article-title":"NewWave: a scalable R\/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data","volume":"38","author":"Agostinis","year":"2022","journal-title":"Bioinformatics"},{"key":"2024081404511934900_btae494-B2","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with Bioconductor","volume":"17","author":"Amezquita","year":"2020","journal-title":"Nat Methods"},{"key":"2024081404511934900_btae494-B3","first-page":"1267","author":"Chen","year":"2013"},{"key":"2024081404511934900_btae494-B4","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/BF02294339","article-title":"Generalized bilinear models","volume":"61","author":"Choulakian","year":"1996","journal-title":"Psychometrika"},{"key":"2024081404511934900_btae494-B5","first-page":"617","article-title":"A generalization of principal components analysis to the exponential family","volume":"14","author":"Collins","year":"2001","journal-title":"Adv Neural Inf Process Syst"},{"key":"2024081404511934900_btae494-B6","first-page":"3367","article-title":"Matrix completion and low-rank SVD via fast alternating least squares","volume":"16","author":"Hastie","year":"2015","journal-title":"J Mach Learn Res"},{"key":"2024081404511934900_btae494-B7","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1080\/10618600.2019.1594835","article-title":"Damped Anderson acceleration with restarts and monotonicity control for accelerating EM and EM-like algorithms","volume":"28","author":"Henderson","year":"2019","journal-title":"J Comput Graph Stat"},{"key":"2024081404511934900_btae494-B8","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1016\/j.ajhg.2022.09.008","article-title":"FastRNA: an efficient solution for PCA of single-cell RNA-sequencing data based on a batch-accounting count model","volume":"109","author":"Lee","year":"2022","journal-title":"Am J Hum Genet"},{"key":"2024081404511934900_btae494-B9","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-1-0716-1307-8_18","volume-title":"RNA Bioinformatics","author":"Linderman","year":"2021"},{"key":"2024081404511934900_btae494-B10","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-3242-6","volume-title":"Generalized Linear Models","author":"McCullagh","year":"1989","edition":"2nd edn"},{"key":"2024081404511934900_btae494-B11","author":"Miller"},{"key":"2024081404511934900_btae494-B12","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","article-title":"A revised airway epithelial hierarchy includes CFTR-expressing ionocytes","volume":"560","author":"Montoro","year":"2018","journal-title":"Nature"},{"key":"2024081404511934900_btae494-B13","author":"Nicol","year":"2023"},{"key":"2024081404511934900_btae494-B14","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1038\/s41588-021-00873-4","article-title":"Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis","volume":"53","author":"Sarkar","year":"2021","journal-title":"Nat Genet"},{"key":"2024081404511934900_btae494-B15","author":"Savarese","year":"2021"},{"key":"2024081404511934900_btae494-B16","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2024081404511934900_btae494-B17","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1186\/s13059-019-1898-6","article-title":"Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis","volume":"20","author":"Sun","year":"2019","journal-title":"Genome Biol"},{"key":"2024081404511934900_btae494-B18","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1186\/s13059-019-1861-6","article-title":"Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model","volume":"20","author":"Townes","year":"2019","journal-title":"Genome Biol"},{"key":"2024081404511934900_btae494-B19","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s13059-019-1900-3","article-title":"Benchmarking principal component analysis for large-scale single-cell RNA-sequencing","volume":"21","author":"Tsuyuzaki","year":"2020","journal-title":"Genome Biol"},{"key":"2024081404511934900_btae494-B20","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/s10107-015-0892-3","article-title":"Coordinate descent algorithms","volume":"151","author":"Wright","year":"2015","journal-title":"Math Program"},{"key":"2024081404511934900_btae494-B21","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae494\/58758934\/btae494.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/8\/btae494\/58813740\/btae494.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/8\/btae494\/58813740\/btae494.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T04:51:52Z","timestamp":1723611112000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae494\/7729117"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,8]]},"references-count":21,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae494","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,8]]},"published":{"date-parts":[[2024,8]]},"article-number":"btae494"}}