Machine Learning for Integrative Genomics lab

All

17 repositories

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
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
•3•28•2•0•Updated Nov 27, 2024Nov 27, 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•1•Updated Nov 27, 2024Nov 27, 2024
.github
Public
home page
2•0•0•0•Updated Nov 15, 2024Nov 15, 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
•3•38•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•18•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