Tools
Algorithms
Integration of Multi-Omics
SIMO
Description: A computational method, which performs Spatial Integration of Multi-Omics single-cell datasets through probabilistic alignment.
Link: https://github.com/ZJUFanLab/SIMO
SCOTCH
Description: A Single-Cell multi-modal integration method leveraging the Optimal Transport algorithm and a cell matCHing strategy.
Link: https://github.com/ZJUFanLab/SCOTCH
Spatial omics tools
scCube
Description: An SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT data.
Link: https://github.com/ZJUFanLab/scCube
SpaTrio
Description: A computational tool based on optimal transport that can align single-cell multi-omics data in space while preserving the spatial topology of the tissue section and local geometry of modality.
Link: https://github.com/ZJUFanLab/SpaTrio
SpaTalk
Description: Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data.
Link: https://github.com/ZJUFanLab/SpaTalk
bulk2space
Description: A spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles.
Link: https://github.com/ZJUFanLab/bulk2space
Single cell omics tools
scRank
Description: A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic data.
Link: https://github.com/ZJUFanLab/scRank
scDeepSort
Description: Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network.
Link: https://github.com/ZJUFanLab/scDeepSort
scCrossTalk
Description: Infer and visualize cell-cell communication for single-cell RNA-seq data.
Link: https://github.com/multitalk/scCrossTalk
scCATCH
Description: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data.
Link: https://github.com/ZJUFanLab/scCATCH
Mass spectra tools
MASSKG
Description: A knowledge-based computational tool for annotating mass spectra of natural products and discovering novel structures from crude extracts.
Link: https://xomics.com.cn/masskg
Database
CellTalkDB
Description: A manually curated database of literature-supported ligand-receptor interactions in human and mouse.
Link: http://tcm.zju.edu.cn/celltalkdb
IdCHD
Description: A comprehensive resource and online toolkit for coronary heart disease-centric medical research.
Link: https://github.com/SpaTrek/idCHD