Software

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Work in progress

We are currently adding the software corresponding to LBMC projects.

To add your software please fill out this form:

 

LiCre

Team PhysBioChrom
Python
Theoretical Physics
Polymer Physics
Data Analysis
LiCre
analysis and simulation pipeline written in python
Nov 25, 2025
Léo Tarbouriech, Mohammed Badazze, Hélène Duplus, Gael Yvert

 

LiCre

Team PhysBioChrom
Python
Theoretical Physics
Polymer Physics
Data Analysis
LiCre
analysis and simulation pipeline written in python
Nov 25, 2025
Léo Tarbouriech

 

FACSCeCYL

Team Piazza
R
FACS
fitting of Cell-cycle phases in FACS DNA stained histograms
Nov 24, 2025
Bulteau Romain

 

RAPToR

Team Francesconi
R
RNA-seq
Statistics
NGS
Real Age Prediction from Transcriptome staging on Reference
Nov 24, 2025
Bulteau Romain, Francesconi Mirko

 

CARDAMOM

Team SBDM
Python
GRN
single-cell
Inference of mechanistic GRN from time-stamped single-cell expression data
Nov 18, 2025
Elias Ventre

 

ExonOntology

Team Regards
MySQL
RNA-Seq
webapp
Splicing
Exon Ontology is a web interface to predict the functional consequences of alternative splicing variations.
Nov 18, 2025
Léon-Charles Tranchevent, Fabien Aubé, Louis Dulaurier, Clara Benoit-Pilven, Amandine Rey, Arnaud Poret, Emilie Chautard, Hussein Mortada, François-Olivier Desmet, Fatima Zahra Chakrama, Maira Alejandra Moreno-Garcia, Evelyne Goillot, Stéphane Janczarski, Franck Mortreux, Cyril F Bourgeois, Didier Auboeuf

 

FasterDB

Team Regards
MySQL
RNA-Seq
webapp
Splicing
web interface that describes known splice variants of human and mouse protein coding genes
Nov 18, 2025
Pierre Mallinjoud, Jean-Philippe Villemin, Hussein Mortada, Micaela Polay Espinoza, François-Olivier Desmet, Samaan Samaan, Emilie Chautard, Léon-Charles Tranchevent, Didier Auboeuf

 

MyLabStocks

database
plasmids
strains,
cell lines
oligonucleotides
molecular biology
PHP
MySQL
Team GCLS
A web application dedicated to managing stocks of molecular biology laboratories
Nov 18, 2025
Stéphane Janczarski, Florent Chuffart, Guillaume Pommier, Gael Yvert

 

Nanoseq_splicing_improved

Team Regards
Nextflow
RNA-Seq
Nanoport
improvement/modification of the nf-core nanoseq pipeline
Nov 18, 2025
William Desaintjean

 

delfies

Team Delattre
Genomics
Python
Querying genomes for evidence of Programmed DNA Elimination
Nov 18, 2025
Brice Letcher, Marie Delattre

 

oligo4ssHic

Hi-C
ssHi-C
Rust
Team Piazza
a small rust program to generate oligonucleotides for single-strand Hi-C experiments
Nov 18, 2025
Laurent Modolo

 

ssHiCstuff

Hi-C
ssHi-C
Python
Team Piazza
Software to handle ssDNA-specific Hi-C data
Nov 18, 2025
Nicolas Mendiboure, Loqmen Anani, Laurent Modolo, Aurèle Piazza

 

Vast-tools_multi_nf

Team Regards
Nextflow
RNA-Seq
Splicing
NGS
complete analysis with the software Vast-tools
Nov 18, 2025
Mehdi Marchand, William Desaintjean, Hélène Polveche

pipeline schema

HiC Meta pipeline available

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

 

DESeq2-wrapper

R
Team ReGArDS
Wrapper to ease the use of DESeq2 to perform differential expression analysis
Sep 25, 2024
Nicolas Fontrodona

 

TopGO-wrapper

R
Team ReGArDS
Wrapper to ease the use of TopGO to perform gene ontology enrichment analysis
Sep 25, 2024
Nicolas Fontrodona

 

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

 

kmerclust

Statistics
R
Team Delattre
Search for sequences eliminated in the genome of M. belari by coverage ratio and clustering
Oct 21, 2022
Marie Delattre, Laurent Modolo, Ghislain Durif

 

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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