Gagneur lab

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53 repositories

dependencies_DNALM
Public
Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements
Jupyter Notebook
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MIT License
•1•11•3•0•Updated Mar 13, 2025Mar 13, 2025
scooby
Public
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
Python
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MIT License
•1•18•2•2•Updated Mar 13, 2025Mar 13, 2025
drop
Public
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
rna-seq genetic-diagnosis pipeline
Python
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MIT License
•47•139•36•4•Updated Mar 7, 2025Mar 7, 2025
OUTRIDER
Public
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
rna-seq r diagnostics outlier-detection mendelian-genetics expression-analysis count-data
R
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MIT License
•11•50•15•1•Updated Mar 5, 2025Mar 5, 2025
FRASER
Public
FRASER - Find RAre Splicing Events in RNA-seq
r diagnostics outlier-detection splicing rare-disease aberrant-splicing rna-seq
R
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MIT License
•22•43•25•0•Updated Mar 4, 2025Mar 4, 2025
drop_demo_data
Public
1•0•0•0•Updated Mar 2, 2025Mar 2, 2025
Watershed
Public
Prioritization of functional rare genetic variants by integrating genomic annotations and RNA-seq
Jupyter Notebook
•12•0•0•0•Updated Feb 26, 2025Feb 26, 2025
abexp-ukbb-prs
Public
Python
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MIT License
•0•0•0•0•Updated Feb 26, 2025Feb 26, 2025
abexp-ukbb-variant-clumping
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Feb 26, 2025Feb 26, 2025
abexp-ukbb-trait-analysis
Public
UK Biobank trait analysis with AbExp scores
Python
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MIT License
•0•1•0•0•Updated Feb 26, 2025Feb 26, 2025
AbExp
Public
Python
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MIT License
•1•4•0•0•Updated Feb 26, 2025Feb 26, 2025
wBuild
Public
R project report builder
bioinformatics snakemake wbuild
Python
•6•4•11•6•Updated Feb 26, 2025Feb 26, 2025
AbExp-utils
Public
Python
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MIT License
•0•0•0•0•Updated Feb 20, 2025Feb 20, 2025
PROTRIDER
Public
Python
•0•1•1•0•Updated Feb 10, 2025Feb 10, 2025
funcRVP
Public
Bayesian genotype to phenotype model leveraging gene embeddings
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Jan 31, 2025Jan 31, 2025
scooby_reproducibility
Public
Jupyter Notebook
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MIT License
•0•4•0•0•Updated Dec 20, 2024Dec 20, 2024
splicemap
Public
Jupyter Notebook
•4•20•2•0•Updated Oct 14, 2024Oct 14, 2024
spectralis
Public
Python
•7•13•5•0•Updated Oct 1, 2024Oct 1, 2024
absplice
Public
Python
•4•36•1•2•Updated Sep 11, 2024Sep 11, 2024
rep
Public
RNA expression prediction
Python
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MIT License
•0•0•0•0•Updated Jul 11, 2024Jul 11, 2024
Leukemia_outlier
Public
R
•0•3•0•0•Updated Jun 10, 2024Jun 10, 2024
FRASER-old-gagneurlab
Public
rna-seq r diagnostics outlier-detection mendelian-genetics splicing-analyses beta-binomial
R
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MIT License
•22•13•0•0•Updated May 13, 2024May 13, 2024
dataviz
Public
Data Analysis and Visualization in R
HTML
•2•1•0•1•Updated Feb 12, 2024Feb 12, 2024
FRASER-2.0-analysis
Public
This repository contains the analysis code for the FRASER 2.0 manuscript.
R
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MIT License
•0•1•2•0•Updated Sep 29, 2023Sep 29, 2023
gene-embedding
Public
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Sep 25, 2023Sep 25, 2023
SpeciesLM
Public
Species-aware DNA language models capture regulatory elements and their evolution
Jupyter Notebook
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MIT License
•1•17•0•0•Updated Aug 21, 2023Aug 21, 2023
AbSplice_analysis
Public
Python
•1•3•0•0•Updated Aug 18, 2023Aug 18, 2023
spliceai_rocksdb
Public
Python
•1•0•0•0•Updated Jun 1, 2023Jun 1, 2023
MMSplice_MTSplice
Public
Tissue-specific variant effect predictions on splicing
machine-learning variant-effect-prediction splicing vep-plugin
Jupyter Notebook
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MIT License
•21•40•10•4•Updated May 23, 2023May 23, 2023
snakemake-slurm-template
Public
Python
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MIT License
•1•0•0•0•Updated May 11, 2023May 11, 2023