Machine Learning for Integrative Genomics lab

All

24 repositories

Circe
Public
Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.
gene-regulation atac-seq graphical-lasso single-cell-atac-seq cis-regulatory-elements
Python
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Other
•2•33•1•0•Updated Feb 1, 2026Feb 1, 2026
ReCoN
Public
Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations
single-cell treatment-effects biological-networks multicellular
Python
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GNU General Public License v3.0
•0•5•0•0•Updated Jan 30, 2026Jan 30, 2026
DynamicNetworkExplorer
Public
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Jan 23, 2026Jan 23, 2026
Xpressor
Public
fork of scPRINT for the Xpressor and ESM2-finetuning ICML paper
Jupyter Notebook
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MIT License
•0•4•0•0•Updated Jan 22, 2026Jan 22, 2026
.github
Public
home page
2•0•0•2•Updated Jan 20, 2026Jan 20, 2026
CIRCE_reproducibility
Public
Reproducibility code of the Circe (Trimbour et al., 2025) publication
Jupyter Notebook
•0•3•0•0•Updated Jan 18, 2026Jan 18, 2026
CellOracle
Public
This is a lite version of the CellOracle package to run functions necessary to HuMMuS and ReCoN while increasing dependencies flexibility
Python
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Other
•71•1•0•0•Updated Jan 14, 2026Jan 14, 2026
HuMMuS
Public
Molecular interactions inference from single-cell multi-omics data
transcriptomics single-cell biological-networks epigenomics multilayer-networks multi-omics
R
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GNU Affero General Public License v3.0
•6•30•6•0•Updated Jan 14, 2026Jan 14, 2026
scPRINT-2
Public
🏃🏃 Your next-gen single-cell Foundation Model
Jupyter Notebook
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GNU General Public License v3.0
•2•20•0•0•Updated Dec 19, 2025Dec 19, 2025
GRnnData
Public
Awesome GRN enhanced AnnData toolkit
rna-seq utils single-cell gene-regulatory-network anndata scverse
Jupyter Notebook
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MIT License
•2•11•0•1•Updated Dec 19, 2025Dec 19, 2025
scPRINT
Public
🏃 The go-to single-cell Foundation Model
open-source ai embeddings rnaseq sprint zero-shot-learning denoising single-cell-rna-seq cell-biology batch-correction
Jupyter Notebook
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GNU General Public License v3.0
•23•137•3•0•Updated Dec 18, 2025Dec 18, 2025
scconfluence
Public
A novel method for single-cell diagonal integration: scConfluence
integration single-cell dimension-reduction optimal-transport multiomics
Python
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GNU General Public License v3.0
•1•26•2•0•Updated Nov 3, 2025Nov 3, 2025
stories
Public
Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein
Python
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GNU General Public License v3.0
•2•24•0•0•Updated Oct 21, 2025Oct 21, 2025
celloracle_recon
Public
Lite version of CellOracle (Morris-Lab) to make it compatible with ReCoN and HuMMuS
0•0•0•0•Updated Sep 22, 2025Sep 22, 2025
Mowgli
Public
Single-cell multi-omics integration using Optimal Transport
matrix-factorization single-cell dictionary-learning optimal-transport multi-omics multi-omics-integration
Python
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GNU General Public License v3.0
•5•50•0•0•Updated Aug 14, 2025Aug 14, 2025
benGRN
Public
Awesome Benchmark of Gene Regulatory Networks
Jupyter Notebook
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GNU General Public License v3.0
•2•0•0•0•Updated Jan 27, 2025Jan 27, 2025
scPRINT-old1
Public archive
Single Cell Pretrained Regulatory network INference from Transcripts
Jupyter Notebook
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GNU General Public License v3.0
•1•11•0•0•Updated Sep 17, 2024Sep 17, 2024
scDataLoader
Public
a dataloader to work with large single cell datasets from lamindb
Jupyter Notebook
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GNU General Public License v3.0
•5•0•0•0•Updated Sep 16, 2024Sep 16, 2024
stories_reproducibility
Public
STORIES: Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein
Jupyter Notebook
•1•4•0•0•Updated Jul 9, 2024Jul 9, 2024
mowgli_reproducibility
Public
Data and scripts to reproduce experiments for Mowgli.
matrix-factorization reproducibility single-cell dictionary-learning optimal-transport multi-omics
Python
•1•6•1•0•Updated Apr 1, 2024Apr 1, 2024
scc_reproducibility
Public
Jupyter Notebook
•0•4•1•0•Updated Feb 29, 2024Feb 29, 2024
momix-notebook
Public
Jupyter Notebook
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GNU General Public License v3.0
•14•66•3•1•Updated Nov 14, 2023Nov 14, 2023
OT-scOmics
Public
This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell om…
biology gpu single-cell optimal-transport
Python
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GNU General Public License v3.0
•8•43•0•0•Updated Feb 3, 2023Feb 3, 2023
scNET
Public
jupyther notebook comparing reproducibility of single-cell network inference algorithms
Jupyter Notebook
•2•4•2•1•Updated Sep 15, 2021Sep 15, 2021