Code

https://github.com/statbiophys/IGoR

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

References

Q. Marcou, T. Mora*, A. M. Walczak*, High-throughput immune repertoire analysis with IGoR, Nature Communications 9 561 (2018) [pdf] [arXiv]

https://github.com/statbiophys/SONIA

SONIA is a python software developed to infer selection pressures on features of amino acid CDR3 sequences. The inference is based on maximizing the likelihood of observing a selected data sample given a representative pre-selected sample.

References

G. Isacchini, Z. Sethna, Y. Elhanati, A. Nourmohammad, A.M. Walczak, T. Mora, On generative models of T-cell receptor sequences, arXiv (2019)

Z. Sethna, G. Isacchini, T. Dupic, T. Mora, A.M. Walczak, Y. Elhanati, Population variability in the generation and thymic selection of T-cell repertoires, arXiv (2019)

https://github.com/pogorely/ALICE

ALICE detects TCR involved in immune responses from single RepSeq datasets.

References

M. V. Pogorelyy, A. A. Minervina, M. Shugay, D. M. Chudakov, Y. B. Lebedev*, T. Mora*, A. M. Walczak*, Detecting T-cell receptors involved in immune responses from single repertoire snapshots. PLoS Biology 17(6):e3000314 (2019) [pdf] [arXiv]

https://github.com/statbiophys/Immprint

webapp

https://immprint.herokuapp.com/

Immprint is a command-line tool built to identify the origine of T-cell samples. Given two samples of TCR sequences it decides whether they come from the same individual or not.

References

T. Dupic, M. Bensouda Koraichi, A. A. Minervina, M. V. Pogorelyy, T. Mora*, A. M. Walczak*, Immune fingerprinting, arxiv.org/abs/2006.13530 (2020)

https://github.com/statbiophys/sonnia

SoNNia is a python 3.6 software which extends the functionality of the SONIA package. It expands the choice of selection models that can be inferred. Non linear single-chain models and (non-)linear paired-chain models are included in the package.

References

Isacchini G, Walczak AM, Mora T, Nourmohammad A, Deep generative selection models of T and B cell receptor repertoires with soNNia, (2020) bioRxiv,

https://bitbucket.org/yuvalel/repgenhmm

repgenHMM is a C++ software designed to infer V(D)J recombination using dynamic programming.

References

Y. Elhanati, Q. Marcou, T. Mora and A. M. Walczak, repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data, Bioinformatics 32(13) 1943 (2016) [pdf] [arXiv]

https://github.com/yuvalel/PUBLIC

PUBLIC is a set of Python scripts for analyzing sharing of TCRs, and predict public clones

References

Y. Elhanati, Z. Sethna, G. G. Callan Jr., T. Mora*, A.M. Walczak*, Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination, Immunological Reviews 284(1) 167-179 (2018) [pdf] [arXiv]

https://github.com/statbiophys/MaxEnt_Model_Population_Coupling

MATLAB repository for learning models of neural population activity where individual firing rates are coupled to the population firing rate.

References

C. Gardella, O. Marre*, T. Mora*, A tractable method for describing complex couplings between neurons and population rate, eNeuro 3(4) e0160-15.2016 (2016) [pdf] [arXiv]

https://github.com/statbiophys/RBM_TRBM

MATLAB code to learn generative models of collective neural activity using a Restricted Boltzmann Machine (RBM) and Temporal Restricted Boltzmann Machine (TRBM).

References

C. Gardella, O. Marre*, T. Mora*, Blindfold learning of an accurate neural metric, Proc Natl Acad Sci 115 (13) 3267 (2018) [pdf] [arXiv]

https://github.com/huytran216/LiveFly_toolbox

A toolbox for the analysis of transcription dynamics in live Drosophila melanogaster embryos. The toolbox allows users to process two-color 3D confocal movies acquired using nuclei-labeling and the fluorescent RNA-tagging system described in the previous chapter and export the nuclei’s position as a function of time, their lineages and the intensity traces of the active loci.

References

1. H. Tran, C.A. Perez-Romero, T. Ferraro, C. Fradin, N. Dostatni, M. Coppey*, A.M Walczak*, LiveFly - a toolbox for the analysis of transcription dynamics in live Drosophila embryos, Methods in Molecular Biology (2018).