{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T14:49:45Z","timestamp":1775832585342,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,6]],"date-time":"2023-10-06T00:00:00Z","timestamp":1696550400000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","award":["R01 HG009937"],"award-info":[{"award-number":["R01 HG009937"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["CCF-1750472"],"award-info":[{"award-number":["CCF-1750472"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["CNS-1763680"],"award-info":[{"award-number":["CNS-1763680"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry\u2019s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Simpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https:\/\/github.com\/COMBINE-lab\/simpleaf, and via bioconda. Documentation for simpleaf is available at https:\/\/simpleaf.readthedocs.io\/en\/latest\/ and tutorials for simpleaf that have been developed can be accessed at https:\/\/combine-lab.github.io\/alevin-fry-tutorials.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad614","type":"journal-article","created":{"date-parts":[[2023,10,6]],"date-time":"2023-10-06T22:27:19Z","timestamp":1696631239000},"source":"Crossref","is-referenced-by-count":21,"title":["<tt>simpleaf<\/tt>\n                    : a simple, flexible, and scalable framework for single-cell data processing using alevin-fry"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8259-7434","authenticated-orcid":false,"given":"Dongze","family":"He","sequence":"first","affiliation":[{"name":"Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology , University of Maryland , College Park, MD, 20742, United 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