Cancer Python Packages

aihw-mcp

Query the Australian Institute of Health and Welfare in plain English from Claude or any MCP client. Mortality (GRIM/MORT), cancer incidence, health expenditure, youth justice detention, and the public hospitals register.

trisicell

No description available

pvactools

A cancer immunotherapy tools suite

lymph-model

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

agfusion

Python package to annotate and visualize gene fusions.

coderdata

Dataset package for facile training and testing of machine learning/AI algorithms that predict drug response in cancer model systems.

portpy

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

scmalignantfinder

scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells from their normal counterparts.

lyscripts

Scripts and utilities for commonly used tasks related to the modelling of lymphatic tumor progression.

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

meddatasets

The meddatasets library contains clinical research datasets, cancer diagnostic records, chronic disease statistics, smoking and cancer risk data, worldwide COVID-19 case records, water pollution and disease impact data, and much more.

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

pasmopy

Patient-Specific Modeling in Python

panoptes-he

A multi-resolution CNN to predict cancer histopathologic features

pymaftools

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

celligner

A useful module for alligning cell lines to tumors

med-minds

🧠 | Multimodal Integration of Oncology Data System

fings

Filters for Next Generation Sequencing

gdc-api-wrapper

Genomic Data Commons API wrapper

dnavi

DNA fragmentation analysis from electropherograms

probabilistic2020

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

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.

macrodna

A high-accuracy tool for integrating scDNA-seq and scRNA-seq data