ZJUFanLab

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

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

scNiche

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

scSpace

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

TCMChat

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

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.

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

SpaTrio

SCOTCH

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

MSformer

A novel molecular representation framework via meta structures

scTITANS

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

scDeepTalk

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

SIMO

scDisProcema

SRTBenchmark

Benchmarking spatial clustering methods for spatial resolved transcriptomics

SAMBA

scCrossTalk

Infer cell-cell communications based on CellTalkDB

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

GT-MRL

PerturbMerge

PerturbMeta

PerturbScore