Dr. FAN, Xiaohui

scCATCH. Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

bulk2space. a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

scDeepSort. Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

SpaTalk. Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

scRank. 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

TCMChat. Repo for TCMChat: A Generative Large Language Model for Traditional Chinese Medicine

scNiche. a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution

CellTalkDB. A manually curated database of literature-supported ligand-receptor interactions in human and mouse

scCube. an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT data

scSpace. an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references

MSformer. A novel molecular representation framework via meta structures

SIMO. Jupyter Notebook

scCATCH_performance_comparison. The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database

scDeepSort_performance_comparison. The source code and results for different methods on annotating external testing datsets of human and mouse.

SpaTrio. Python

KANO. Code and data for the Nature Machine Intelligence paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt".

CCL-cGPS. A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research

SRTBenchmark. Benchmarking spatial clustering methods for spatial resolved transcriptomics

scTITANS. Identifying key genes and cell subclusters for time-series single cell sequencing data

SCOTCH. SCOTCH is a Single-Cell multi-modal integration method leveraging the Optimal Transport algorithm and a cell matCHing strategy

TCMNet. Python

TRACE. Python

Subtypist. Subtypist is a computational toolkit for subtype identification of single-cell transcriptomic data without reference.

scDeepTalk. Infer cell-cell communications based on feed-forward neural network

scDisProcema. R

SAMBA.

scCrossTalk. R

WAVE. Jupyter Notebook