Software

Single Cell Multiomics

• MetroSCREEN   is computational workflow for predicting metabolic activities and regulomes from single-cell RNA-seq data.
• Cisformer   is a cross-attention-based model for single-cell cross-modality generation between gene expression and chromatin accessibility.
• SCRIPro   is a tool for evaluating gene regulatory network activities for both single-cell and spatial transcriptomics and multiomics.
• SCRIP   is a tool for evaluating gene regulatory network activities in scATAC-seq data.
• SELINA   is a deep learning-based framework for cell-type annotation of human scRNA-seq data using large-scale curated references.
• SCREE   is a workflow to perform quality control and analyses of multimodal single-cell CRISPR screen datasets.

Spatial Multiomics

• Cellist   is a computational method for accurate cell segmentation and signal enhancement on high-resolution spatial transcriptomics.
• STRIDE   is a topic-model-based deconvolution method for low-resolution spatial transcriptomics by integrating with scRNA-seq.
• CCI   Benchmark of CCI prediction tools based on the integration of single-cell and spatial transcriptomic data.

Single Cell Resources

• MetroTIME   serves as a comprehensive resource detailing the metabolic heterogeneities and their associated regulomes in pan-cancer fibroblasts and myeloid cells.
• TabulaTIME   is a comprehensive tumor microenvironment landscape by integrating single-cell and spatial transcriptomic data.
• TISCH   is a scRNA-seq database that includes over 6M human and mouse tumor scRNA-seq cells, and provides detailed cell-type annotation and gene expression visualization across different cancer types.
• HUSCH   is a scRNA-seq database that includes over 3M human normal scRNA-seq cells from 41 tissue/organs, and provides detailed cell-type annotation and gene expression visualization across different tissue/organs.