Gagneur lab

All

55 repositories

funcRVP
Public
Bayesian genotype to phenotype model leveraging gene embeddings
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated Aug 15, 2025Aug 15, 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
•51•151•41•4•Updated Aug 14, 2025Aug 14, 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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Other
•24•47•27•0•Updated Aug 14, 2025Aug 14, 2025
AbExp
Public
Python
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MIT License
•1•8•0•1•Updated Aug 14, 2025Aug 14, 2025
AbExp-web
Public
HTML
•0•0•0•0•Updated Aug 12, 2025Aug 12, 2025
scooby
Public
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
Python
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MIT License
•4•29•1•2•Updated Aug 8, 2025Aug 8, 2025
absplice2
Public
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Jul 29, 2025Jul 29, 2025
splicemap
Public
Jupyter Notebook
•4•21•2•0•Updated Jul 29, 2025Jul 29, 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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Other
•14•53•15•0•Updated Jul 28, 2025Jul 28, 2025
PROTRIDER
Public
Python
•3•3•0•1•Updated Jul 7, 2025Jul 7, 2025
absplice
Public
Python
•4•39•1•2•Updated Jul 3, 2025Jul 3, 2025
AbSplice2_analysis
Public
Jupyter Notebook
•0•0•0•0•Updated Jul 2, 2025Jul 2, 2025
tMAE
Public
R
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MIT License
•5•1•0•0•Updated Jun 3, 2025Jun 3, 2025
scooby_reproducibility
Public
Jupyter Notebook
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MIT License
•1•4•0•0•Updated Jun 1, 2025Jun 1, 2025
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•14•3•0•Updated Mar 13, 2025Mar 13, 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
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
spectralis
Public
Python
•8•14•5•0•Updated Oct 1, 2024Oct 1, 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
•24•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•2•2•0•Updated Sep 29, 2023Sep 29, 2023
gene-embedding
Public
Jupyter Notebook
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MIT License
•1•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•19•1•0•Updated Aug 21, 2023Aug 21, 2023
AbSplice_analysis
Public
Python
•1•3•0•0•Updated Aug 18, 2023Aug 18, 2023