Pinned Repositories
HILARy
Python package for inference of lineages in antibody repertoires
HLAGuessr
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.
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
pygor3
pygor3 repository
RBM_TRBM
RBM, TRBM and neural metrics
SONIA
Infer selection pressures on features of amino acid CDR3 sequences.
soNNia
Statistical Biophysics Consortium's Repositories
statbiophys/OLGA
Compute generation probabilities of CDR3 amino acid and nucleotide sequences
statbiophys/SONIA
Infer selection pressures on features of amino acid CDR3 sequences.
statbiophys/HLAGuessr
statbiophys/soNNia
statbiophys/pygor3
pygor3 repository
statbiophys/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.
statbiophys/HILARy
Python package for inference of lineages in antibody repertoires
statbiophys/olha
A package to generate TCR/BCR sequences fast, based on olga
statbiophys/catede
Tools for information theoretic measures estimation.
statbiophys/ENS-survival-kit
Useful tools for your life at ENS
statbiophys/IGoR
IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:
statbiophys/shmoof
Models of somatic hypermutation based on out-of-frame sequences
statbiophys/SOS
Simple Olga & Sonia (SOS)
statbiophys/STAR
Single Time-point Antibody Recognition
statbiophys/zebrafishGC
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.
statbiophys/ATrieGC
A python/c++ module to store large amount of sequences and look at hamming distance clustering
statbiophys/HIV_coevo
Data processing and modeling for HIV and BCR longitudinal data
statbiophys/indie
Probabilistic alignment software to deal with indels in Ig receptor sequences.
statbiophys/MINIMALIST
Companion Github of the MINIMALIST preprint.
statbiophys/thymic_development_2022
Population based selection shapes the T cell receptor repertoire during thymic development
statbiophys/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.
statbiophys/Inferring_TCR_repertoire_dynamics
Repository associated with the paper "Inferring and predicting the T-cells repertoire dynamics of healthy individuals"
statbiophys/Global_and_Local_Variability_2023
statbiophys/Immune-fingerprinting
Companion github to the "Immune fingerprinting" paper
statbiophys/paper-viral-immune-coevo-theory
statbiophys/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)
statbiophys/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).
statbiophys/social_mice
Python and MATLAB code and data for statistical physics analysis of social behavior in Eco-HAB mice.
statbiophys/tools
Repository where useful tools can be reused by others in the group
statbiophys/viral_coevo
Figures and results of the paper "Evolutionary stability of antigenically escaping viruses"