ZJUFanLab/SpaTalk

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

Language: R - Size: 9.83 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 70 - Forks: 18

ZJUFanLab/scCATCH

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

Language: R - Size: 52 MB - Last synced at: 2 days ago - Pushed at: about 2 years ago - Stars: 227 - Forks: 36

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

Language: R - Size: 23.5 MB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 46 - Forks: 5

ZJUFanLab/SIMO

Language: Jupyter Notebook - Size: 13.7 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 4 - Forks: 3

ZJUFanLab/scDeepSort

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

Language: Python - Size: 19.4 MB - Last synced at: 2 days ago - Pushed at: almost 2 years ago - Stars: 103 - Forks: 19

ZJUFanLab/CellTalkDB

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

Language: R - Size: 18.5 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 30 - Forks: 5

ZJUFanLab/MSformer

A novel molecular representation framework via meta structures

Language: Jupyter Notebook - Size: 21.4 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

ZJUFanLab/scNiche

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

Language: Jupyter Notebook - Size: 12.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

ZJUFanLab/SRTBenchmark

Benchmarking spatial clustering methods for spatial resolved transcriptomics

Language: Python - Size: 706 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

ZJUFanLab/scDeepSort_performance_comparison

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

Language: R - Size: 6.33 MB - Last synced at: 2 days ago - Pushed at: about 4 years ago - Stars: 12 - Forks: 0

ZJUFanLab/bulk2space

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

Language: Jupyter Notebook - Size: 12.1 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 115 - Forks: 23

ZJUFanLab/TCMChat

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

Language: Python - Size: 7.74 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 3

ZJUFanLab/scTITANS

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

Language: R - Size: 21.5 KB - Last synced at: 2 days ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 0

ZJUFanLab/SCOTCH

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

Language: Jupyter Notebook - Size: 5.11 MB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

ZJUFanLab/scCube

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

Language: Jupyter Notebook - Size: 71 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 6 - Forks: 0

ZJUFanLab/scCrossTalk

Language: R - Size: 11.9 MB - Last synced at: 2 days ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

ZJUFanLab/PerturbMeta

Language: R - Size: 32.2 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ZJUFanLab/PerturbScore

Language: R - Size: 15.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ZJUFanLab/PerturbMerge

Language: Python - Size: 23.4 KB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ZJUFanLab/scSpace

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

Language: HTML - Size: 29.6 MB - Last synced at: 11 months ago - Pushed at: almost 2 years ago - Stars: 19 - Forks: 3

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

Language: HTML - Size: 4.89 MB - Last synced at: 2 days ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 12

ZJUFanLab/CCL-cGPS

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

Language: R - Size: 593 KB - Last synced at: 2 days ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 1

ZJUFanLab/SpaTrio

Language: Python - Size: 74.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

ZJUFanLab/KANO Fork of HICAI-ZJU/KANO

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

Language: Python - Size: 17.3 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 0

ZJUFanLab/scDeepTalk

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

Language: R - Size: 14.4 MB - Last synced at: 2 days ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

ZJUFanLab/scDisProcema

Language: R - Size: 3.15 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

ZJUFanLab/SAMBA

Size: 1000 Bytes - Last synced at: 2 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

ZJUFanLab/awesome-single-cell Fork of seandavi/awesome-single-cell

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

Size: 1.23 MB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0