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@statbiophys Statistical Biophysics Consortium

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    39 repositories

    • HILARy

      Public
      Python package for inference of lineages in antibody repertoires
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•7•0•3•Updated Apr 16, 2026Apr 16, 2026

    • TT-inhibition

      Public
      Code for the T-to-T cell inhibition project
      Jupyter Notebook
      •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • Paraplume

      Public
      Python
      •
      Other
      •0•17•0•0•Updated Mar 2, 2026Mar 2, 2026

    • STAR

      Public
      Single Time-point Antibody Recognition
      Jupyter Notebook
      •0•6•1•0•Updated Feb 12, 2026Feb 12, 2026

    • ConstrainedPromoters

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • memory_plasmab_dynamics

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • pygor3

      Public
      pygor3 repository
      Jupyter Notebook
      •
      Other
      •5•10•5•3•Updated Nov 20, 2025Nov 20, 2025

    • soNNia

      Public
      Python
      •
      GNU General Public License v3.0
      •4•18•7•0•Updated Nov 18, 2025Nov 18, 2025

    • OLGA

      Public
      Compute generation probabilities of CDR3 amino acid and nucleotide sequences
      Python
      •
      GNU General Public License v3.0
      •17•65•12•0•Updated Nov 18, 2025Nov 18, 2025

    • ABGen

      Public
      Code for the Paper: Generative Model for Monoclonal Antibodies
      Python
      •
      Other
      •1•5•0•0•Updated Jun 2, 2025Jun 2, 2025

    • HLAGuessr

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•19•1•0•Updated Apr 20, 2025Apr 20, 2025

    • 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

    • 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

    • SONIA

      Public
      Infer selection pressures on features of amino acid CDR3 sequences.
      Python
      •
      GNU General Public License v3.0
      •8•25•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

    • 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-infecte…
      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…
      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 ge…
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•3•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
      •26•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" …
      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:/…
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 31, 2022Jan 31, 2022
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