{"doi":"10.1093/bioinformatics/btae494","title":"Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca","abstract":"SUMMARY: Motivated by theoretical and practical issues that arise when applying Principal component analysis (PCA) to count data, Townes et al. introduced \"Poisson GLM-PCA\", 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 \"Alternating Poisson Regression\" (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. AVAILABILITY AND IMPLEMENTATION: 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.","journal":"Bioinformatics","year":2024,"id":451642,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9463,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":106843,"name":"Peter Carbonetto","orcid":"0000-0003-1144-6780","position":1,"is_corresponding":false},{"id":5157,"name":"Matthew Stephens","orcid":"0000-0001-5397-9257","position":2,"is_corresponding":false},{"id":1273050,"name":"Eric Weine","orcid":"0009-0001-7809-1649","position":0,"is_corresponding":true}],"reference_count":20,"raw_metadata":null,"created_at":"2026-07-19T02:02:45.951080Z","pmid":"39110511","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}