joannadreux

cutadapt

Cutadapt removes adapter sequences from sequencing reads

hammock

Cluster up to millions of peptide sequences on shared sequence motifs.

aoi

Ghost in the Shell powered by OpenAI (Terminal version of ChatGPT)

tcr-bert

Large language modeling applied to T-cell receptor (TCR) sequences.

DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

pretty-jupyter

Creates dynamic html report from jupyter notebook.

MHCfovea

IPDMHC

Github for files currently published in the IPD-MHC FTP Directory hosted at the European Bioinformatics Institute

alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

SCALOP

ANARCI

Antibody Numbering and Antigen Receptor ClassIfication

mhcgnomes

Parsing MHC nomenclature in the wild

Gooey

Turn (almost) any Python command line program into a full GUI application with one line

ipython-sql

%%sql magic for IPython, hopefully evolving into full SQL client

amazon-redshift-python-driver

Redshift Python Connector. It supports Python Database API Specification v2.0.

sqlalchemy-redshift

Amazon Redshift SQLAlchemy Dialect

mhcflurry

Peptide-MHC I binding affinity prediction

mhctools

Python interface to running command-line and web-based MHC binding predictors

pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

MIMOSCA

A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.

OCEAN

OCEAN - Optimized Cross rEActivity estimatioN

DeepImmuno

Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity

TITAN

Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2021)

TAPE

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

CAR-T

Clonal kinetics and single-cell transcriptional profiling of adoptively transferred CD19-specific CD8+ CAR-T cells

CytoTalk

A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.

tcrdist2

Quantifiable predictive features define epitope-specific T cell receptor repertoires

iSMART

Highly specific clustering of T cell receptor CDR3s

vdjmatch

⚙️ Matching T-cell repertoire against a database of TCR antigen specificities

tcr-dist

Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)