Immunology Python Packages

flowio

A Python library for reading and writing Flow Cytometry Standard (FCS) files

arda-mapper

High-throughput mapping and domain partitioning of antigen receptor sequences

vdjtools

Analysis of immune repertoire sequencing results

flowkit

A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

lzgraphs

Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.

deeptcr

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

tidytcells

Standardise TR/MH/IG data

copepodtcr

COmbinatorial PEptide POoling for TCR specificity

immunedb

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

aims-immune

AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below site for documentation

immuno-compass

Generalizable AI predicts immunotherapy outcomes across cancers and treatments

stitchr

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

sceptr

Highly informative TCR representation model

epitopepredict

Python package and command line tool for epitope prediction

vquest

Automate IMGT V-QUEST usage on imgt.org

decombinator

Decombinator: fast, error-correcting analysis of TCR repertoires

pygempick

Open Source python module to enable batch gold particle picking, filtering, processing & statistical modelling of TEM images produced by IGEM (immunogold electron microscopy).

pybatman

Bayesian inference of Activation of TCR by Mutant Antigens

mhc-tp

Peptides motif search tool and Source protein mappers

icepop

Immune cell population analysis tool for estimating immune cell composition from gene expression data (DEGs or raw counts). Python CLI + web interface for deconvolution, visualization, and Circos plots.