checkdyn 0.1.0

Modeling treatment-induced immune checkpoint dynamics

CheckDyn

CheckDyn models treatment-induced immune checkpoint dynamics to predict adaptive resistance to immune checkpoint blockade (ICB) therapy.

Overview

CheckDyn is a computational biology pipeline that:

• Collects paired pre/post-treatment RNA-seq data from GEO cohorts (≥8 datasets, ≥150 paired samples)
• Detects compensatory checkpoint upregulation patterns during ICB treatment
• Models temporal checkpoint gene dynamics via a Transformer architecture
• Predicts early adaptive resistance (target AUROC ≥ 0.75)

Installation

pip install checkdyn

Usage

# Collect datasets
checkdyn collect --output data/

# Run full analysis
checkdyn analyze --input data/ --output results/

# Predict resistance for a patient
checkdyn predict --model pretrained --input patient.csv

Key Datasets

Dataset	Cancer	Platform	GEO
Riaz2017	Melanoma	RNA-seq	GSE91061
Gide2019	Melanoma	RNA-seq	GSE91061
Chen2016	Melanoma	RNA-seq	GSE79691
Sade-Feldman2018	Melanoma	scRNA-seq	GSE120575
Yost2019	BCC	scRNA-seq	GSE123813
Caushi2021	NSCLC	scRNA-seq	GSE176021
Hanna2018	HNSCC	NanoString	GSE112927

License

MIT