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Gagneur lab (@gagneurlab)

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drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

OUTRIDER

OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data

MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing

Jupyter Notebook

FRASER

FRASER - Find RAre Splicing Events in RNA-seq

absplice

concise

Concise: Keras extension for regulatory genomics

Jupyter Notebook

FRASER-analysis

Accompanying analysis code for the FRASER manuscript

splicemap

Jupyter Notebook

SpeciesLM

Jupyter Notebook

spectralis

OCR-Stats

MMSplice_paper

Analysis code of MMSplice paper

Jupyter Notebook

wBuild

R project report builder

dependencies_DNALM

Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements

Jupyter Notebook

rCube

AbSplice_analysis

OUTRIDER-analysis

Accompanying analysis repository for the OUTRIDER paper

Manuscript_Avsec_Bioinformatics_2017

Code for Avsec et al, Bioinformatics 2017

Jupyter Notebook

ALS-kaggle

Outlier prediction-based solution to Task1 of the End ALS Kaggle challenge

Jupyter Notebook

py_outrider

py_outrider: a generalized framework for context-dependent outlier detection in omics data

gfeat

Python genomic features extractor from raw files

autoCorrection

The autoencoder implementation for the OUTRIDER package

Jupyter Notebook

gene-embedding

Jupyter Notebook

Leukemia_outlier

dataviz

Data Analysis and Visualization in R

AbExp

RNA_diagnostics_paper_figures

Manuscript_Cheng_RNA_2017

Analysis code for Cheng et al., RNA (2017)

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".

Jupyter Notebook

abexp-ukbb-trait-analysis

UK Biobank trait analysis with AbExp scores