Projects in Awesome Lists by gagneurlab
A curated list of projects in awesome lists by gagneurlab .
https://github.com/gagneurlab/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
genetic-diagnosis pipeline rna-seq
Last synced: 27 Jan 2025
https://github.com/gagneurlab/outrider
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
count-data diagnostics expression-analysis mendelian-genetics outlier-detection r rna-seq
Last synced: 08 May 2025
https://github.com/gagneurlab/fraser
FRASER - Find RAre Splicing Events in RNA-seq
aberrant-splicing diagnostics outlier-detection r rare-disease rna-seq splicing
Last synced: 04 Apr 2025
https://github.com/gagneurlab/mmsplice_mtsplice
Tissue-specific variant effect predictions on splicing
machine-learning splicing variant-effect-prediction vep-plugin
Last synced: 11 Apr 2025
https://github.com/gagneurlab/concise
Concise: Keras extension for regulatory genomics
Last synced: 11 Apr 2025
https://github.com/gagneurlab/fraser-analysis
Accompanying analysis code for the FRASER manuscript
outlier-detection r rare-disease rna-seq snakemake workflow
Last synced: 11 Apr 2025
https://github.com/gagneurlab/specieslm
Species-aware DNA language models capture regulatory elements and their evolution
Last synced: 11 Apr 2025
https://github.com/gagneurlab/dependencies_dnalm
Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements
Last synced: 11 Apr 2025
https://github.com/gagneurlab/wbuild
R project report builder
bioinformatics snakemake wbuild
Last synced: 11 Apr 2025
https://github.com/gagneurlab/mmsplice_paper
Analysis code of MMSplice paper
Last synced: 11 Apr 2025
https://github.com/gagneurlab/manuscript_avsec_bioinformatics_2017
Code for Avsec et al, Bioinformatics 2017
Last synced: 19 Mar 2025
https://github.com/gagneurlab/als-kaggle
Outlier prediction-based solution to Task1 of the End ALS Kaggle challenge
Last synced: 19 Mar 2025
https://github.com/gagneurlab/outrider-analysis
Accompanying analysis repository for the OUTRIDER paper
Last synced: 19 Mar 2025
https://github.com/gagneurlab/cellular_energy_codon_analysis
Code for the data processing and analyses present on the manuscript: "Cellular energy regulates mRNA translation and degradation in a codon-specific manner".
Last synced: 19 Mar 2025
https://github.com/gagneurlab/autocorrection
The autoencoder implementation for the OUTRIDER package
autoencoder expression-analysis outlier-detection pyhton rna-seq
Last synced: 11 Apr 2025
https://github.com/gagneurlab/py_outrider
py_outrider: a generalized framework for context-dependent outlier detection in omics data
Last synced: 11 Apr 2025
https://github.com/gagneurlab/gfeat
Python genomic features extractor from raw files
Last synced: 11 Apr 2025
https://github.com/gagneurlab/funcrvp
Bayesian genotype to phenotype model leveraging gene embeddings
Last synced: 19 Mar 2025
https://github.com/gagneurlab/manuscript_cheng_rna_2017
Analysis code for Cheng et al., RNA (2017)
Last synced: 19 Mar 2025
https://github.com/gagneurlab/abexp-ukbb-trait-analysis
UK Biobank trait analysis with AbExp scores
Last synced: 19 Mar 2025
https://github.com/gagneurlab/cagi6_sickkids
Code repository of the CAGI 6 Sickkids challenge: Predicting molecular events underlying disease from a patient’s genome and transcriptome using variant annotation, aberrant gene expression events, and human phenotype ontology.
Last synced: 19 Mar 2025
https://github.com/gagneurlab/fraser-2.0-analysis
This repository contains the analysis code for the FRASER 2.0 manuscript.
Last synced: 19 Mar 2025