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ZJUFanLab

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

scCATCH

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

210

bulk2space

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

Jupyter Notebook

110

scDeepSort

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

Python

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

scSpace

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

HTML

scCube

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

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

HTML

scDeepSort_performance_comparison

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

CCL-cGPS

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

SpaTrio

Python

SCOTCH

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

Jupyter Notebook

TCMChat

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

Python

scDeepTalk

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

scTITANS

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

scDisProcema

SAMBA

scCrossTalk

ZJUFanLab/scNiche

ZJUFanLab

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