Machine Learning for Integrative Genomics lab

All

17 repositories

scPRINT
Public
single cell foundation model for Gene network inference and more
open-source embeddings rnaseq zero-shot-learning denoising single-cell-rna-seq cell-biology batch-correction gene-regulatory-network celltype-annotation
Jupyter Notebook
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MIT License
•5•35•1•0•Updated Dec 12, 2024Dec 12, 2024
GRnnData
Public
Awesome GRN enhanced AnnData toolkit
rna-seq utils single-cell gene-regulatory-network anndata scverse
Jupyter Notebook
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GNU General Public License v3.0
•2•3•0•0•Updated Dec 12, 2024Dec 12, 2024
.github
Public
home page
2•0•0•0•Updated Dec 3, 2024Dec 3, 2024
Circe
Public
Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).
gene-regulation atac-seq graphical-lasso single-cell-atac-seq cis-regulatory-elements
Python
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GNU Affero General Public License v3.0
•1•18•2•0•Updated Nov 28, 2024Nov 28, 2024
benGRN
Public
Awesome Benchmark of Gene Regulatory Networks
Jupyter Notebook
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GNU General Public License v3.0
•1•0•0•0•Updated Nov 13, 2024Nov 13, 2024
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
•4•22•2•0•Updated Nov 6, 2024Nov 6, 2024
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
•4•0•0•0•Updated Sep 16, 2024Sep 16, 2024
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•39•4•0•Updated Sep 6, 2024Sep 6, 2024
stories
Public
Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein
Python
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GNU General Public License v3.0
•0•10•0•0•Updated Aug 21, 2024Aug 21, 2024
scconfluence
Public
A novel method for single-cell diagonal integration: scConfluence
integration single-cell dimension-reduction optimal-transport multiomics
Python
•0•19•0•0•Updated Jul 13, 2024Jul 13, 2024
stories_reproducibility
Public
STORIES: Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein
Jupyter Notebook
•0•3•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•3•0•0•Updated Apr 1, 2024Apr 1, 2024
scc_reproducibility
Public
Jupyter Notebook
•0•2•1•0•Updated Feb 29, 2024Feb 29, 2024
momix-notebook
Public
Jupyter Notebook
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GNU General Public License v3.0
•11•63•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 omics data.
biology single-cell optimal-transport gpu
Python
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GNU General Public License v3.0
•7•37•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