{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T14:12:27Z","timestamp":1768745547319,"version":"3.49.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,1,25]],"date-time":"2025-01-25T00:00:00Z","timestamp":1737763200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 angioimmunoblastic T cell lymphoma and primary central nervous system lymphoma, elucidating tumor boundaries. HemaScope is freely available at https:\/\/zhenyiwangthu.github.io\/HemaScope_Tutorial\/.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf002","type":"journal-article","created":{"date-parts":[[2025,1,25]],"date-time":"2025-01-25T13:08:01Z","timestamp":1737810481000},"source":"Crossref","is-referenced-by-count":5,"title":["HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9407-0135","authenticated-orcid":false,"given":"Zhenyi","family":"Wang","sequence":"first","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1738-2466","authenticated-orcid":false,"given":"Yuxin","family":"Miao","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing National Research Center for Information Science and Technology, Bioinformatics Division, Department of Automation, Tsinghua University , Beijing 100084,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8057-6186","authenticated-orcid":false,"given":"Hongjun","family":"Li","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing National Research Center for Information Science and Technology, Bioinformatics Division, Department of Automation, Tsinghua University , Beijing 100084,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4347-5981","authenticated-orcid":false,"given":"Wenyan","family":"Cheng","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1108-4233","authenticated-orcid":false,"given":"Minglei","family":"Shi","sequence":"additional","affiliation":[{"name":"Institute of Medical Innovation and Research, Peking University Third Hospital , Beijing 100191,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2573-8813","authenticated-orcid":false,"given":"Gang","family":"Lv","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-6937-1955","authenticated-orcid":false,"given":"Yating","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201210,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0725-1000","authenticated-orcid":false,"given":"Junyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6268-782X","authenticated-orcid":false,"given":"Tingting","family":"Tan","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3968-8036","authenticated-orcid":false,"given":"Jin","family":"Gu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing National Research Center for Information Science and Technology, Bioinformatics Division, Department of Automation, Tsinghua University , Beijing 100084,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7022-6115","authenticated-orcid":false,"given":"Michael Q","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas , Richardson, TX 75080-3021,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2349-208X","authenticated-orcid":false,"given":"Jianfeng","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3961-8572","authenticated-orcid":false,"given":"Hai","family":"Fang","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2968-7665","authenticated-orcid":false,"given":"Zhu","family":"Chen","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3789-1284","authenticated-orcid":false,"given":"Saijuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Research Unit of Hematologic Malignancies Genomics and Translational Research of Chinese Academy of Medical Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,1,25]]},"reference":[{"key":"2025092421513148400_qzaf002-B1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41592-019-0691-5","article-title":"Single-cell multimodal omics: the power of many","volume":"17","author":"Zhu","year":"2020","journal-title":"Nat 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