Cancer Python Packages

glam-radiomics

Gray Level Affinity Metrics (GLAM)

lymph-model

Python package for statistical modelling of lymphatic metastatic spread in head & neck cancer.

pvactools

A cancer immunotherapy tools suite

trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

agfusion

Python package to annotate and visualize gene fusions.

coderdata

A package to download, load, and process multiple benchmark multi-omic drug response datasets

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

lyscripts

Package to interact with lymphatic progression data and models.

portpy

Opensource Python project for cancer radiation treatment planning [AAPM'23]

scmalignantfinder

A tool for identitying malignant cells from single-cell RNA-seq data

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

matchminer-ai

MatchMiner-AI package

pymaftools

A Python toolkit for MAF files and multi-omics cancer genomics — parsing, analysis, ML, and publication-ready visualization.

meddatasets

A curated collection of medical and healthcare datasets for data analysis, clinical research, epidemiology, and education. Includes cancer data, chronic disease diagnostics, hospital management records, public health, statistics and more from Kaggle sources.

pasmopy

Patient-Specific Modeling in Python

panoptes-he

A multi-resolution CNN to predict cancer histopathologic features

celligner

tumor - cancer cell line alignment. Use it on the depmap portal or install it with pip.

dnavi

Cell-free DNA fragmentation analysis directly from electrophoresis data

med-minds

🧠 | Multimodal Integration of Oncology Data System

probabilistic2020

Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test

fings

Filters for Next Generation Sequencing

gdc-api-wrapper

A simple Python wrapper for the GDC Application Programming Interface

ctdna

ctdna computes the expected tumor detection size at a given sampling frequency.

oncomark

A deep learning tool designed to predict Cancer Hallmark activities from tumor biopsy samples.