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62 repositories

fedeca
Public
Code repository associated with the FedECA article
survival-analysis causal-inference federated-learning
Python
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Other
•3•11•9•2•Updated Aug 20, 2025Aug 20, 2025
histoplus
Public
Python
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Other
•1•20•1•1•Updated Aug 20, 2025Aug 20, 2025
docker-dependency-updater
Public
Checks system dependencies and update them if required
environment--production bu--dept-data-platform owner--squad-dse
TypeScript
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Apache License 2.0
•0•1•0•0•Updated Aug 19, 2025Aug 19, 2025
PyDESeq2
Public
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
python bioinformatics rna-seq transcriptomics differential-expression
Python
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MIT License
•77•666•38•7•Updated Aug 19, 2025Aug 19, 2025
fedpydeseq2
Public
A federated implementation of PyDESeq2, based on Substra.
python bioinformatics rna-seq transcriptomics differential-expression federated-learning
Python
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MIT License
•0•13•0•1•Updated Aug 18, 2025Aug 18, 2025
fedpydeseq2-paper-experiments
Public
Python
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MIT License
•0•0•0•1•Updated Aug 18, 2025Aug 18, 2025
fedpydeseq2-datasets
Public
Python
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MIT License
•0•0•0•1•Updated Aug 18, 2025Aug 18, 2025
dinov3-owkin
Public
Reference PyTorch implementation and models for DINOv3
Jupyter Notebook
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Other
•249•0•0•0•Updated Aug 14, 2025Aug 14, 2025
deepdeconv-fork
Public
Deep probabilistic analysis of single-cell omics data
Python
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BSD 3-Clause "New" or "Revised" License
•401•2•0•2•Updated Aug 5, 2025Aug 5, 2025
deepdeconv-fork-fork
Public
Deep probabilistic analysis of single-cell omics data
Python
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BSD 3-Clause "New" or "Revised" License
•401•0•0•0•Updated Jul 29, 2025Jul 29, 2025
philips-isyntax-rs
Public
Rust bindings for Philips Pathology SDK
bu--dept-diagnostics-tools environment--production owner--hichamazimani
Rust
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Apache License 2.0
•4•0•0•0•Updated Jul 23, 2025Jul 23, 2025
PyDeconv
Public
Python implementation of bulk RNAseq deconvolution algorithms
python bioinformatics rnaseq deconvolution
Python
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Other
•0•41•0•0•Updated Jul 21, 2025Jul 21, 2025
nnUNet
Public
Forking the nnunet repository to be able to develop and modify functionalities.
Python
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Apache License 2.0
•2.1k•0•0•0•Updated Jul 8, 2025Jul 8, 2025
gdm-hackathon
Public
Python
•0•0•0•0•Updated Jul 5, 2025Jul 5, 2025
tsm
Public
Code and data for the paper "Robust sensitivity control in digital pathology via tile score distribution matching", published in MICCAI 2025.
Python
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Other
•0•0•0•0•Updated Jun 30, 2025Jun 30, 2025
plism-benchmark
Public
Official repository for PLISM robustness benchmark of pathology foundation models (MICCAI 2025)
Python
•1•9•0•0•Updated Jun 6, 2025Jun 6, 2025
cytocommunity_ofta
Public
A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from cell phenotypes.
Jupyter Notebook
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MIT License
•14•0•0•0•Updated Jun 4, 2025Jun 4, 2025
TRIDENT
Public
Toolkit for large-scale whole-slide image processing.
Python
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Other
•60•1•0•0•Updated May 5, 2025May 5, 2025
owkin-eva
Public
Evaluation framework for oncology foundation models (FMs)
Python
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Apache License 2.0
•20•1•0•0•Updated May 2, 2025May 2, 2025
Patho-Bench
Public
Standardized benchmark for computational pathology foundation models.
Python
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Other
•18•1•0•0•Updated Apr 3, 2025Apr 3, 2025
legitimate-uq-metrics
Public
This repository contains the code implementation to reproduce the experiments presented in our paper on uncertainty quantification metrics for classification tasks.
Python
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MIT License
•0•1•0•0•Updated Mar 4, 2025Mar 4, 2025
Open-Reasoner-Zero
Public
Official Repo for Open-Reasoner-Zero
Python
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MIT License
•111•0•0•0•Updated Mar 3, 2025Mar 3, 2025
sparsesurv
Public
Python
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BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Feb 18, 2025Feb 18, 2025
gbm_hackathon
Public
Python
•8•3•0•0•Updated Jan 31, 2025Jan 31, 2025
HE2TEAD
Public
Python
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Other
•0•0•0•0•Updated Nov 26, 2024Nov 26, 2024
geosketch
Public
Geometry-preserving random sampling
Python
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MIT License
•11•0•0•0•Updated Oct 29, 2024Oct 29, 2024
drl-evaluation
Public
Robust evaluation of DRL methods for survival and gene essentiality prediction on bulk RNAseq
Python
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MIT License
•2•5•2•0•Updated Sep 28, 2024Sep 28, 2024
GrAIdient
Public
GrAIdient is a deep learning framework that aims at challenging the way we train and run models.
bu--dept-diagnostics-tools environment--development owner--jeanfrancoisreboud
Swift
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MIT License
•2•80•0•0•Updated Sep 3, 2024Sep 3, 2024
OAH-Clone-Test
Public
Test Clone Logs
environment--development bu--dept-data-platform owner--oalhajjar
0•0•0•0•Updated Aug 19, 2024Aug 19, 2024
deepdeconv
Public
Deep probabilistic analysis of single-cell omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•401•0•0•0•Updated Aug 13, 2024Aug 13, 2024