Software

Warning

Work in progress

We are currently adding the software corresponding to LBMC projects.

pipeline schema

HiC Meta pipeline available

Hi-C
NGS
pipeline
Nextflow
How to use the nextflow HiC meta pipeline
Dec 6, 2024
Mia Croiset

 

hawkesgenomics

NGS
R
Team SBDM
Statistics
Quantifying spatial dependence in Genomic data with the Hawkes process
Jan 1, 2024
Franck Picard, Laurent Modolo

 

SplicingLore

webapp
Team ReGArDS
A web resource for studying the regulation of cassette exons by human splicing factors
Dec 21, 2023
Hélène Polvèche, Jessica Valat, Nicolas Fontrodona, Didier Auboeuf, Cyril Bourgeois

 

Git Borg LinKer

Team Biocomputing Hub
Rust
done
Outil de sauvegarde incrémentielle des résultats
Feb 23, 2023
Nicolas Fontrodona, Laurent Modolo

 

bamcalib

Team Bernard
Rust
ChIP-seq
NGS
process bam files from a calibrated Chip-Seq analysis
Nov 9, 2022
Pascal Bernard, Laurent Modolo

 

bigwig2bam

Team Bernard
Rust
NGS
tools to generate synthetic bam file from a bigwig file and the corresponding fasta file.
Nov 9, 2022
Pascal Bernard, Laurent Modolo

 

calibrated Chip-Seq analaysis

Team Bernard
Nextflow
ChIP-seq
pipeline
NGS
Nextflow pipeline for calibrated Chip-Seq analysis
Nov 9, 2022
Pascal Bernard, Léonard Colin, Laurent Modolo, Arnaud Duvermy

 

Half-life

scRNA-seq
R
Team SBDM
script to merge data about protein half-life
Sep 8, 2022
Olivier Gandrillon, Laurent Modolo

 

HTRfit

NGS
R
Team GCLS
Statistics
Modèles, simulation et pipeline d’analyse pour quantifier l’interaction entre Génotype et Environment à partir de données massives de RNA-seq.
May 31, 2022
Fabien DUVEAU, Arnaud Duvermy, Gaël Yvert, Laurent Modolo

 

DamID-seq

pipeline
Nextflow
NGS
Team GCLS
pipeline for the analysis of DamID-seq data
Jan 5, 2022
Daniel Jost, Nathan Lecouvreur, Noémie Quesnel, Gaël Yvert, Laurent Modolo

 

Monopoly

Python
pipeline
nextflow
Statistics
Team RMI2
analyse de type Machine learning permettant de modéliser la distribution des ribosomes dans les fractions monosome et polysome
Apr 27, 2021
Emiliano Ricci, David Cluet, Laurent Modolo

 

Mapping Noise

pipeline
Nextflow
Python
BSA-Seq
Team GCLS
Identification de mutations affectant la variabilité d’expression par BSA-Seq
Jun 18, 2020
Fabien Duveau, Julie Kleine-Schultjann, Laurent Modolo

 

MarsSeq pipeline

NGS
scRNA-seq
Team SBDM
Nextflow
pipeline
Pipeline for analyzing single-cell RNA-seq data from the MarsSeq protocol
Mar 9, 2020
Camille Fourneaux, Margaux Prieux, Olivier Gandrillon, Sandrine Giraud, Laurent Modolo

 

TDD

Statistics
R
Team RMI2
Identification de codons (ou d’autres caractéristiques des transcrits) impliqués dans le mécanisme de dégradation traduction-dépendant
Jan 1, 2020
Emiliano Ricci, Emmanuel Labaronne, David Cluet, Laurent Modolo

 

Drosophila haplotype RNA-seq analysis

pipeline
Nextflow
Francesconi Team
pipeline that calls the genetic variants between two haplotypes, constructs the haplotype specific references, maps the Hi-C and RNA-seq data onto the custom reference sequences, estimates haplotype specific gene expression and chromatin contacts
Nov 28, 2019
Francesconi Mirko, Laurent Modolo

 

Tad enrichment

R
Team ReGArDS
Script to test whether a set of exons is enriched in some TADs
Oct 24, 2019
Nicolas Fontrodona, Sebastien Lemaire, Didier Auboeuf, Laurent Modolo

 

salmonInYeast

NGS
Nextflow
pipeline
Team GCLS
Pipeline to study Salmon genome contamination in S. cerevisiae NGS datasets
May 9, 2019
Gael Yvert, Lauren Picard, Laurent Modolo

 

Flexi-Splitter

Python
NGS
Team RMI2
a flexible tool to sort reads into different fastq files from a barcode list and to manage barcodes and UMI in fastq files
Dec 3, 2018
Emmanuel Labaronne, Laurent Modolo

 

criblejurkat

R
Team PRIO
Moanalyse systématique des fichiers de données brutes obtenus sur le cytomètre VYB Masquant afin de mieux normaliser les données
Oct 24, 2017
Pierre Jalinot, Armelle Roisin, Laurent Modolo

 

readthrough

NGS
Nextflow
pipeline
Team Bernard
Readthrough detection and quantification pipeline
Aug 9, 2017
Pascal Bernard, Laurent Modolo
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