ZJUFanLab

bulk2space

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

CellTalkDB

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

scCATCH

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

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

scCube

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

scDeepSort

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

scDeepSort_performance_comparison

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

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

scSpace

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

SpaTalk

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

ZJUFanLab/scCATCH

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

ZJUFanLab/bulk2space

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

ZJUFanLab/scDeepSort

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

ZJUFanLab/SpaTalk

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

ZJUFanLab/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

ZJUFanLab/CellTalkDB

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

ZJUFanLab/scSpace

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

ZJUFanLab/scCube

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

ZJUFanLab/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

ZJUFanLab/scDeepSort_performance_comparison

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

ZJUFanLab/KANO

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

ZJUFanLab/CCL-cGPS

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

ZJUFanLab/SpaTrio

ZJUFanLab/SCOTCH

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

ZJUFanLab/TCMChat

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

ZJUFanLab/scNiche

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

ZJUFanLab/scTITANS

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

ZJUFanLab/scDeepTalk

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

ZJUFanLab/scDisProcema

ZJUFanLab/SAMBA

ZJUFanLab/scCrossTalk

Infer cell-cell communications based on CellTalkDB

ZJUFanLab/awesome-single-cell

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

ZJUFanLab/GT-MRL

ZJUFanLab/PerturbMerge

ZJUFanLab/PerturbMeta

ZJUFanLab/PerturbScore

ZJUFanLab/SIMO