biostudies-literatureUnknown3(2)Zhang YSingle-cell RNA-seq data analysis generally requires quality control, normalization, highly variable genes screening, dimensionality reduction and clustering. Among these processes, downstream analysis including dimensionality reduction and clustering are sensitive to the selection of highly variable genes. Though increasing number of tools for selecting the highly variable genes have been developed, an evaluation of their performances and a general strategy are lack. Here, we compare the performance of nine commonly used methods for screening variable genes by using single-cell RNA-seq data from hematopoietic stem/progenitor cells and mature blood cells, and find that SCHS outperforms other methods regarding to reproducibility and accuracy. However, this method prefers the selection of hiBlood science (Baltimore, Md.)35-39https://www.ebi.ac.uk/biostudies/studies/S-EPMC8974938biostudies-literatureSIEVE: identifying robust single cell variable genes for single-cell RNA sequencing data.PMC8974938Zhu PXie XZhang YWu PfalseSIEVE: identifying robust single cell variable genes for single-cell RNA sequencing data.Single-cell RNA-seq data analysis generally requires quality control, normalization, highly variable genes screening, dimensionality reduction and clustering. Among these processes, downstream analysis including dimensionality reduction and clustering are sensitive to the selection of highly variable genes. Though increasing number of tools for selecting the highly variable genes have been developed, an evaluation of their performances and a general strategy are lack. Here, we compare the performance of nine commonly used methods for screening variable genes by using single-cell RNA-seq data from hematopoietic stem/progenitor cells and mature blood cells, and find that SCHS outperforms other methods regarding to reproducibility and accuracy. However, this method prefers the selection of hi2021-01-01T00:00:00Z2021 Apr2026-05-30T15:04:50.899Z2025-04-04T23:04:26.955ZS-EPMC89749383540283210.1097/BS9.0000000000000072