Cancer Python Packages

glam-radiomics

Gray Level Affinity Metrics (GLAM)

pvactools

A cancer immunotherapy tools suite

mhcmatch

Ultrafast MHC binding prediction and epitope's mimic search. Immunogenicity scorer. Designing personalised cancer vaccine cassettes

trisicell

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

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

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]

agfusion

Python package to annotate and visualize gene fusions.

lymph-model

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

lyscripts

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

pasmopy

Patient-Specific Modeling in Python

survscope

Static, reproducible TCGA Kaplan-Meier survival plots with compact plot-only data

scmalignantfinder

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

pymaftools

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

panoptes-he

A multi-resolution CNN package to predict endometrial cancer features

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

matchminer-ai

Python package for the MatchMiner-AI cancer clinical trial matching inference workflow.

insilico-cancer-center

Simulate the evolution and treatment of tumors and generate bulk, single-cell and spatial data from them.

celligner

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

deepspotm

Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.

med-minds

🧠 | Multimodal Integration of Oncology Data System

dnavi

Cell-free DNA fragmentation analysis directly from electrophoresis data

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