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atriegc

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

bnabs_prob

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.

catede

Tools for information theoretic measures estimation.

compare_selection_models_2019

On generative models of T cell receptor sequences

ens-survival-kit

Useful tools for your life at ENS

global_and_local_variability_2023

hilary

Python package for inference of lineages in antibody repertoires

hiv_coevo

Data processing and modeling for HIV and BCR longitudinal data

hlaguessr

igor

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

immprint

ImmPrint answers the question "were these two samples extracted from the same individual ?" by looking at the numbers and sequences of shared unique TCR between the two samples.

immune-fingerprinting

Companion github to the "Immune fingerprinting" paper

indie

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

inferring_tcr_repertoire_dynamics

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

maxent_model_population_coupling

Maximum Entropy model for P(sigma_i, K)

minimalist

Companion Github of the MINIMALIST preprint.

noiset

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.

olga

Compute generation probabilities of CDR3 amino acid and nucleotide sequences

olha

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

paper-viral-immune-coevo-theory

pygor3

pygor3 repository

rbm_trbm

RBM, TRBM and neural metrics

repository-sharing-paper

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)

seqam

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).

shmoof

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

social_mice

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

sonia

Infer selection pressures on features of amino acid CDR3 sequences.

sonnia

sos

Simple Olga & Sonia (SOS)

star

Single Time-point Antibody Recognition