Gagneur lab

All

53 repositories

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•41•22•1•Updated Feb 14, 2025Feb 14, 2025
AbExp
Public
Python
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MIT License
•1•3•0•1•Updated Feb 13, 2025Feb 13, 2025
PROTRIDER
Public
Python
•0•1•0•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
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
•46•139•37•4•Updated Jan 16, 2025Jan 16, 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 Jan 10, 2025Jan 10, 2025
scooby_reproducibility
Public
Jupyter Notebook
•
MIT License
•0•4•0•0•Updated Dec 20, 2024Dec 20, 2024
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•49•15•1•Updated Dec 11, 2024Dec 11, 2024
splicemap
Public
Jupyter Notebook
•4•19•2•0•Updated Oct 14, 2024Oct 14, 2024
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•2•0•Updated Oct 4, 2024Oct 4, 2024
spectralis
Public
Python
•7•13•5•0•Updated Oct 1, 2024Oct 1, 2024
AbExp-utils
Public
Python
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MIT License
•1•0•0•0•Updated Sep 21, 2024Sep 21, 2024
absplice
Public
Python
•4•33•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
abexp-ukbb-trait-analysis
Public
UK Biobank trait analysis with AbExp scores
Python
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MIT License
•0•1•0•0•Updated Jul 5, 2024Jul 5, 2024
Leukemia_outlier
Public
R
•0•2•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
Watershed
Public
Prioritization of functional rare genetic variants by integrating genomic annotations and RNA-seq
Jupyter Notebook
•12•0•0•0•Updated May 9, 2024May 9, 2024
wBuild
Public
R project report builder
bioinformatics snakemake wbuild
Python
•6•4•11•6•Updated May 3, 2024May 3, 2024
dataviz
Public
Data Analysis and Visualization in R
HTML
•2•1•0•1•Updated Feb 12, 2024Feb 12, 2024
abexp-ukbb-prs
Public
Python
•
MIT License
•0•0•0•0•Updated Oct 12, 2023Oct 12, 2023
abexp-ukbb-variant-clumping
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Oct 12, 2023Oct 12, 2023
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•0•2•0•Updated Sep 29, 2023Sep 29, 2023
gene-embedding
Public
Jupyter Notebook
•
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•16•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
Cellular_energy_codon_analysis
Public
Code for the data processing and analyses present on the manuscript: "Cellular energy regulates mRNA translation and degradation in a codon-specific manner".
Jupyter Notebook
•0•2•0•0•Updated Feb 22, 2023Feb 22, 2023