{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:34Z","timestamp":1772138074296,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T00:00:00Z","timestamp":1744848000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health\/National Institute on Aging"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Spectral flow cytometry provides greater insights into cellular heterogeneity by simultaneous measurement of up to 50 markers. However, analysing such high-dimensional (HD) data is complex through traditional manual gating strategy. To address this gap, we developed CAFEs (Cell Analyzer for Flow Experiments) as an open-source Python-based web application with a graphical user interface. Built with Streamlit, CAFE incorporates libraries such as Scanpy for single-cell analysis, Pandas and PyArrow for efficient data handling, and Matplotlib, Seaborn, Plotly for creating customizable figures. Its robust toolset includes density-based downsampling, dimensionality reduction, batch correction, Leiden-based clustering, cluster merging, and annotation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Using CAFE, we demonstrated analysis of a human PBMC dataset of 350\u00a0000 cells identifying 16 distinct cell clusters. CAFE can generate publication-ready figures in real time via interactive slider controls and dropdown menus, eliminating the need for coding expertise and making HD data analysis accessible to all.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CAFE is licensed under MIT and is freely available at https:\/\/github.com\/mhbsiam\/cafe.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf176","type":"journal-article","created":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T05:40:39Z","timestamp":1744868439000},"source":"Crossref","is-referenced-by-count":1,"title":["CAFE: an integrated web app for high-dimensional analysis and visualization in spectral flow cytometry"],"prefix":"10.1093","volume":"41","author":[{"given":"Md Hasanul Banna","family":"Siam","sequence":"first","affiliation":[{"name":"Department of Pathology, 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