Cancer Python Packages

pvactools

A cancer immunotherapy tools suite

trisicell

No description available

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

agfusion

Python package to annotate and visualize gene fusions.

portpy

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

lyscripts

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

lymph-model

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

coderdata

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

pasmopy

Patient-Specific Modeling in Python

pymaftools

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

scmalignantfinder

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

panoptes-he

A multi-resolution CNN package to predict endometrial cancer features

emmaa

Ecosystem of Machine-maintained Models with Automated 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.

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

celligner

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

gdc-api-wrapper

Genomic Data Commons API wrapper

dnavi

Cell-free DNA fragmentation analysis directly from electrophoresis data

fings

Filters for Next Generation Sequencing

oncomark

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

ctdna

Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding

macrodna

Accurate integration of single-cell DNA and RNA data for a deeper understanding of tumor heterogeneity

tumorevo

Simulate and illustrate tumor evolution under different spatial constraints.