{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:01Z","timestamp":1753875841983,"version":"3.41.2"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,17]],"date-time":"2024-08-17T00:00:00Z","timestamp":1723852800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008136","name":"Case Western Reserve University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008136","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>Recent methodology advances in computational signal deconvolution have enabled bulk transcriptome data analysis at a finer cell-type level. Through deconvolution, identifying cell-type-specific differentially expressed (csDE) genes is drawing increasing attention in clinical applications. However, researchers still face a number of difficulties in adopting csDE genes detection methods in practice, especially in their experimental design. Here we present cypress, the first experimental design and statistical power analysis tool in csDE genes identification. This tool can reliably model purified cell-type-specific (CTS) profiles, cell-type compositions, biological and technical variations, offering a high-fidelity simulator for bulk RNA-seq convolution and deconvolution. cypress conducts simulation and evaluates the impact of multiple influencing factors, by various statistical metrics, to help researchers optimize experimental design and conduct power analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>cypress is an open-source R\/Bioconductor package at https:\/\/bioconductor.org\/packages\/cypress\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae511","type":"journal-article","created":{"date-parts":[[2024,8,17]],"date-time":"2024-08-17T17:26:53Z","timestamp":1723915613000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>cypress<\/i>: an R\/Bioconductor package for cell-type-specific differential expression analysis power assessment"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5494-1960","authenticated-orcid":false,"given":"Shilin","family":"Yu","sequence":"first","affiliation":[{"name":"Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation , Cleveland, OH 44106, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guanqun","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Population and Quantitative Health Sciences, Case Western Reserve University , Cleveland, OH 44106, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3710-9029","authenticated-orcid":false,"given":"Wen","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Population and Quantitative Health Sciences, Case Western Reserve University , Cleveland, OH 44106, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8757-651X","authenticated-orcid":false,"given":"Wenjing","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Michigan , Ann Arbor, MI 48109, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Surgery, Case Western Reserve University , Cleveland, OH 44106, United States"},{"name":"Division of Surgical Oncology, Department of Surgery, University Hospitals Cleveland Medical Center , Cleveland, OH 44106, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiongwei","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Pathology, Case Western Reserve University , Cleveland, OH 44106, United 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