Gao Lab

All

33 repositories

EPS
Public
Quantifying predictability of gene expression from histology image
mutual-information spatial-transcriptomics histology-images spatial-omics
Python
•
MIT License
•0•1•0•0•Updated Nov 16, 2025Nov 16, 2025
GLUE
Public
Graph-linked unified embedding for single-cell multi-omics data integration
bioinformatics deep-learning single-cell single-cell-multiomics
Python
•
MIT License
•66•441•21•0•Updated Nov 10, 2025Nov 10, 2025
DECIPHER
Public
DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data
transformer single-cell-omics spatial-transcriptomics contrastive-learning spatial-omics
Python
•
MIT License
•1•23•0•0•Updated Oct 22, 2025Oct 22, 2025
CASCADE
Public
Causal discovery of gene regulatory programs from single-cell genomics
Python
•
MIT License
•1•12•0•0•Updated Sep 5, 2025Sep 5, 2025
bioconda-recipes
Public
Conda recipes of GLUE for the bioconda channel.
Shell
•
MIT License
•3.7k•0•0•0•Updated Sep 4, 2025Sep 4, 2025
SEERS
Public
Jupyter Notebook
•0•2•0•0•Updated Jun 20, 2025Jun 20, 2025
Guideline-for-Computational-Biology-and-Bioinformatics
Public
100•368•0•0•Updated May 6, 2025May 6, 2025
PASSAGE
Public
Phenotype Associated Spatial Signature Analysis with Graph-based Embedding
bioinformatics deep-learning spatial-transcriptomics
Jupyter Notebook
•
MIT License
•1•25•0•0•Updated Mar 5, 2025Mar 5, 2025
SVEN
Public
Quantifying the regulatory potential of genetic variants via a hybrid sequence-oriented model
Python
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Other
•1•10•0•0•Updated Jan 17, 2025Jan 17, 2025
RA_prediction
Public
Model for RA prediction
Python
•0•1•0•0•Updated Jan 15, 2025Jan 15, 2025
SLAT
Public
Spatial-Linked Alignment Tool
bioinformatics deep-learning spatial-data single-cell single-cell-analysis graph-neural-networks spatial-transcriptomics
Python
•
MIT License
•9•90•0•0•Updated Dec 20, 2024Dec 20, 2024
SPARKLE
Public
HTML
•0•1•0•0•Updated Nov 26, 2024Nov 26, 2024
Gastric-Cancer-Lymph-Node-Metastasis
Public
R
•0•0•0•0•Updated Sep 3, 2024Sep 3, 2024
Cell_BLAST
Public
A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
bioinformatics deep-learning single-cell single-cell-rna-seq
Python
•
MIT License
•13•94•8•0•Updated Jul 23, 2024Jul 23, 2024
SLE-ImmuneAtlas
Public
scRNA and scVDJ analysis for SLE samples
single-cell-analysis single-cell-immune-profiling
Jupyter Notebook
•1•8•0•0•Updated Sep 24, 2023Sep 24, 2023
ProjectManagementWorkshop
Public template
This is a demo repo for project management in Technology Workshop 2023
Python
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MIT License
•0•0•0•0•Updated Aug 25, 2023Aug 25, 2023
LOST_and_FOUND
Public
Python
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Other
•1•13•0•0•Updated Apr 7, 2023Apr 7, 2023
Markonv_figures
Public
Markonv: a novel convolutional layer for identifying inter-positional correlations effectively and efficiently This is the repository for reproducing figures and tables in the paper.
Python
•
MIT License
•1•4•0•0•Updated Dec 11, 2022Dec 11, 2022
HERE
Public
Human Embryonic RNA Editome
R
•0•4•0•0•Updated Dec 1, 2022Dec 1, 2022
Markonv
Public
core code of Markonv layer and Markonv operator
Cuda
•
MIT License
•1•2•0•0•Updated Jun 17, 2022Jun 17, 2022
RiboCalc
Public
RiboCalc data and script
Python
•
Other
•1•6•0•0•Updated May 26, 2022May 26, 2022
vConv-Figures_and_Tables
Public
The repository for reproducing figures and tables in the vConv paper
deep-learning convolutional-neural-networks
Python
•1•2•2•0•Updated Mar 19, 2022Mar 19, 2022
CPC2_standalone
Public
Official repo for the standalone package of Coding Potential Calculator (CPC) 2.
bioinformatics lncrna noncoding long-non-coding cpc2
Python
•
GNU General Public License v3.0
•12•28•2•0•Updated Sep 11, 2021Sep 11, 2021
REVA-Data_Source_Code
Public
Python
•0•0•0•0•Updated Jul 8, 2021Jul 8, 2021
vConv
Public
An implementation of vConv layer.
deep-learning convolutional-neural-networks
Python
•2•11•1•0•Updated Apr 28, 2021Apr 28, 2021
CARMEN
Public
The Standalone package of CARMEN
Python
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Other
•1•1•0•0•Updated Jan 22, 2021Jan 22, 2021
sgRNA
Public
A pipeline for sgRNA design
R
•3•0•0•0•Updated Sep 23, 2020Sep 23, 2020
FunTFBS
Public
A package to identify functional TFBS
transcriptional-regulatory-network tfbs
Perl
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GNU General Public License v3.0
•2•1•0•0•Updated Aug 19, 2020Aug 19, 2020
scRNAseq_Benchmark
Public
Bench-marking classification tools for scRNA-seq data
Python
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MIT License
•62•4•0•0•Updated Mar 4, 2020Mar 4, 2020
ePooling
Public
Expectation pooling: An effective and interpretable method of pooling for predicting DNA-protein binding
Python
•3•17•0•0•Updated Sep 21, 2019Sep 21, 2019