HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells

作者：Zhenyi Wang, Yuxin Miao, Hongjun Li, Wenyan Cheng, Minglei Shi, Lv Gang, Yating Zhu, Junyi Zhang, Tingting Tan, Jin Gu, Michael Q. Zhang, Jianfeng Li, Hai Fang, Zhu Chen, Sai‐Juan Chen · 发表于：Genomics Proteomics & Bioinformatics · 年份：2025 · DOI：10.1093/gpbjnl/qzaf002 · 被引用次数：6 · 研究领域：Single-cell and spatial transcriptomics、T-cell and B-cell Immunology、Immune cells in cancer

Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) techniques hold great value in evaluating the heterogeneity and spatial characteristics of hematopoietic cells within tissues. These two techniques are highly complementary, with scRNA-seq offering single-cell resolution and ST retaining spatial information. However, there is an urgent demand for well-organized and user-friendly toolkits capable of handling single-cell and spatial information. Here, we present HemaScope, a specialized bioinformatics toolkit featuring modular designs to analyze scRNA-seq and ST data generated from hematopoietic cells. It enables users to perform quality control, basic analysis, cell atlas construction, cellular heterogeneity exploration, and dynamical examination on scRNA-seq data. Also, it can perform spatial analysis and microenvironment analysis on ST data. Meanwhile, HemaScope takes into consideration hematopoietic cell-specific features, including lineage affiliation evaluation, cell cycle prediction, and marker gene collection. To enhance the user experience, we have deployed the toolkit in user-friendly forms: HemaScopeR (an R package), HemaScopeCloud (a web server), HemaScopeDocker (a Docker image), and HemaScopeShiny (a graphical interface). In case studies, we employed it to construct a cell atlas of human bone marrow, analyze age-related changes, and identify acute myeloid leukemia cells in mice. Moreover, we characterized the microenvironments in angioimmunobla...