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Cancer Python Packages

Python packages with the GitHub topic cancer. Sorted by relevance, with stars and monthly downloads.
griffithlab
pvactools

A cancer immunotherapy tools suite

3K 174 78
faridrashidi
trisicell

No description available

3K 14 2
faridrashidi
scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1
murphycj
agfusion

Python package to annotate and visualize gene fusions.

2K 67 27
PortPy-Project
portpy

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

2K 178 35
lycosystem
lyscripts

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

2K 1 5
lycosystem
lymph-model

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

2K 5 5
PNNL-CompBio
coderdata

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

1K 21 4
pasmopy
pasmopy

Patient-Specific Modeling in Python

759 19 7
xu62u4u6
pymaftools

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

634 7 2
jonyyqn
scmalignantfinder

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

615 18 3
rhong3
panoptes-he

A multi-resolution CNN package to predict endometrial cancer features

575 2 0
indralab
emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

511 11 11
lightbluetitan
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.

337 2 0
lab-rasool
med-minds

🧠 | Multimodal Integration of Oncology Data System

301 9 0
KarchinLab
probabilistic2020

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

264 8 5
BroadInstitute
celligner

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

255 11 9
histolab
gdc-api-wrapper

Genomic Data Commons API wrapper

244 8 0
anjahess
dnavi

Cell-free DNA fragmentation analysis directly from electrophoresis data

189 1 1
cpwardell
fings

Filters for Next Generation Sequencing

180 12 0
SML-CompBio
oncomark

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

120 3 0
reiterlab
ctdna

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

119 13 5
xiru-huang
macrodna

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

117 1 1
pedrofale
tumorevo

Simulate and illustrate tumor evolution under different spatial constraints.

77 7 0
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