scCancer: a package for automated processing of single-cell RNA-seq data in cancer. - Wenbo Guo 010; Dongfang Wang; Shicheng Wang; Yiran Shan; Changyi Liu; Jin Gu (Briefings Bioinform., 2021)

JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding. - Guiying Wu; Xiangyu Li 003; Wenbo Guo 010; Zheng Wei; Tao Hu 001; Yiran Shan; Jin Gu (Briefings Bioinform., 2022)

TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics. - Yiran Shan; Qian Zhang 099; Wenbo Guo 010; Yanhong Wu; Yuxin Miao; Hongyi Xin; Qiuyu Lian; Jin Gu (Genom. Proteom. Bioinform., 2022)

Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. - Haochen Li 003; Tianxing Ma; Minsheng Hao; Wenbo Guo 010; Jin Gu; Xuegong Zhang; Lei Wei (Briefings Bioinform., 2023)

HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC. - Ziming Jiang; Yanhong Wu; Yuxin Miao; Kaige Deng; Fan Yang; Shuhuan Xu; Yupeng Wang; Renke You; Lei Zhang; Yuhan Fan; Wenbo Guo 010; Qiuyu Lian; et al. (Genom. Proteom. Bioinform., 2024)

scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution. - Zeyu Chen; Yuxin Miao; Zhiyuan Tan 007; Qifan Hu; Yanhong Wu; Xinqi Li; Wenbo Guo 010; Jin Gu (Bioinform., 2024)

Computational modeling of single-cell dynamics data. - Wenbo Guo 010; Zeyu Chen; Jin Gu (Briefings Bioinform., 2025)

Inferring cell-type-specific gene regulatory network from cellular transcriptomics data with GeneLink+. - Wei Zhang 241; Bowen Shao; Wenrui Li; Wenbo Guo 010; Jiaxin Lyu; Guangyi Chen; Chuanyuan Wang; Zhi-Ping Liu (Briefings Bioinform., 2025)

scLT-kit: a versatile toolkit for automated processing and analysis of single-cell lineage tracing data. - Wenbo Guo 010; Zeyu Chen; Xinqi Li; Jin Gu (Frontiers Comput. Sci., 2025)