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cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment

Year: 2024
Type: article
Abstract: SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: cypress is an open-source R/Bioconductor package at https://bioconductor.org/packages/cypress/.
DOI: 10.1093/bioinformatics/btae511
Authors: Shilin Yu, Guanqun Meng, Wen Tang, Wenjing Ma, Rui Wang, Xiongwei Zhu, Xiaobo Sun, Hao Feng
Institutions: Cleveland Clinic, Case Western Reserve University, University of Michigan, University Hospitals of Cleveland, University Hospitals Cleveland Medical Center, Zhongnan University of Economics and Law
Language: English
Open Access status: gold
Estimated APC paid: $4,188
OpenAlex ID: W4401665245
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Cites: 23
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Related to: 10