Repositories list

• HILARy

  Public
  Python package for inference of lineages in antibody repertoires

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•5•0•1•Updated Dec 10, 2024Dec 10, 2024

• soNNia

  Public
  Python

  •

  GNU General Public License v3.0

  •4•13•3•0•Updated Dec 10, 2024Dec 10, 2024

• ABGen

  Public
  Code for the Paper: Generative Model for Monoclonal Antibodies

  Python

  •

  Other

  •0•2•0•0•Updated Nov 25, 2024Nov 25, 2024

• social_mice

  Public
  Python and MATLAB code and data for statistical physics analysis of social behavior in Eco-HAB mice.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• HLAGuessr

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•16•1•0•Updated Oct 8, 2024Oct 8, 2024

• ATrieGC

  Public
  A python/c++ module to store large amount of sequences and look at hamming distance clustering

  C++

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Sep 7, 2024Sep 7, 2024

• pygor3

  Public
  pygor3 repository

  Jupyter Notebook

  •

  Other

  •4•9•5•3•Updated Jul 14, 2024Jul 14, 2024

• SONIA

  Public
  Infer selection pressures on features of amino acid CDR3 sequences.

  Python

  •

  GNU General Public License v3.0

  •7•23•1•1•Updated Apr 17, 2024Apr 17, 2024

• tools

  Public
  Repository where useful tools can be reused by others in the group

  0•0•0•0•Updated Apr 8, 2024Apr 8, 2024

• catede

  Public
  Tools for information theoretic measures estimation.

  Python

  •

  Other

  •1•2•0•0•Updated Feb 13, 2024Feb 13, 2024

• ENS-survival-kit

  Public
  Useful tools for your life at ENS

  0•2•0•0•Updated Jan 8, 2024Jan 8, 2024

• STAR

  Public
  Single Time-point Antibody Recognition

  Jupyter Notebook

  •0•3•1•0•Updated Dec 18, 2023Dec 18, 2023

• indie

  Public
  Probabilistic alignment software to deal with indels in Ig receptor sequences.

  C++

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023

• bnabs_prob

  Public
  Scripts for the evaluation of bnabs probabilities of recombination and evolution, according to models learned on Ig sequences from either healthy or hiv-infected donors.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 5, 2023Oct 5, 2023

• NoisET

  Public
  NoisET is an easy-to-use python package that implements and generalizes a previously developed Bayesian method in [Puelma Touzel et al, 2020] ). It can be used to learn experimental noise models for repertoire sequencing from replicates, and to detect responding clones following a stimulus.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•8•0•1•Updated Aug 3, 2023Aug 3, 2023

• viral_coevo

  Public
  Figures and results of the paper "Evolutionary stability of antigenically escaping viruses"

  Jupyter Notebook

  •1•0•0•0•Updated Jul 12, 2023Jul 12, 2023

• zebrafishGC

  Public
  Python and MATLAB code for Granger causality analysis on empirically observed calcium transients in zebrafish neuronal populations, and on synthetic dynamics generated on toy networks.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Jun 21, 2023Jun 21, 2023

• Global_and_Local_Variability_2023

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 20, 2023Mar 20, 2023

• thymic_development_2022

  Public
  Population based selection shapes the T cell receptor repertoire during thymic development

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 31, 2023Jan 31, 2023

• IGoR

  Public
  IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

  C

  •

  GNU General Public License v3.0

  •24•3•0•1•Updated Jan 19, 2023Jan 19, 2023

• HIV_coevo

  Public
  Data processing and modeling for HIV and BCR longitudinal data

  Jupyter Notebook

  •0•1•0•0•Updated Jul 22, 2022Jul 22, 2022

• Repository-Sharing-paper

  Public
  Repository associated with the paper "Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals" (https://www.biorxiv.org/content/10.1101/2021.12.17.473105v1.article-metrics)

  Mathematica

  •0•0•0•0•Updated Jun 16, 2022Jun 16, 2022

• olha

  Public
  A package to generate TCR/BCR sequences fast, based on olga

  C++

  •

  MIT License

  •0•3•0•0•Updated Jun 7, 2022Jun 7, 2022

• Inferring_TCR_repertoire_dynamics

  Public
  Repository associated with the paper "Inferring and predicting the T-cells repertoire dynamics of healthy individuals"

  Jupyter Notebook

  •0•0•0•0•Updated May 2, 2022May 2, 2022

• shmoof

  Public
  Models of somatic hypermutation based on out-of-frame sequences

  Python

  •0•2•0•0•Updated Mar 28, 2022Mar 28, 2022

• seqam

  Public
  Repository associated with the paper "Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints" (https://arxiv.org/abs/2107.12124).

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• OLGA

  Public
  Compute generation probabilities of CDR3 amino acid and nucleotide sequences

  Python

  •

  GNU General Public License v3.0

  •17•49•11•0•Updated Aug 26, 2021Aug 26, 2021

• MINIMALIST

  Public
  Companion Github of the MINIMALIST preprint.

  Python

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Jun 3, 2021Jun 3, 2021

• paper-viral-immune-coevo-theory

  Public
  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 22, 2021Feb 22, 2021

• Immune-fingerprinting

  Public
  Companion github to the "Immune fingerprinting" paper

  Jupyter Notebook

  •0•0•0•0•Updated Oct 4, 2020Oct 4, 2020