cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39153205.
- Also identified by DOI 10.1093/bioinformatics/btae511 and PMC identifier 11357793.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. cypress is an open-source R/Bioconductor package at https://bioconductor.org/packages/cypress/.
Medical subject headings
- Software
- Gene Expression Profiling