56 Open Source Cancer Software Projects

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Personal Cancer Genome Reporter (PCGR)

Detect and visualize target mutations by scanning FastQ files directly

Putting machine learning in the hands of cancer biologists

A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models.

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk/

Building classifiers using cancer transcriptomes across 33 different cancer-types

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

Gene fusion detection and visualization

A Slicer extension to provide a GUI around pyradiomics

Provide R access to the NCI Genomic Data Commons portal.

Web client for CIViC: Clinical Interpretations of Variants in Cancer

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

Backend Server for CIViC Project

3D hotspot mutation proximity analysis tool

An interactive web portal for exploring immuno-oncology data

Python package to annotate and visualize gene fusions.

Flask App for Cancer Donation Portal using basic Python, SQLite3, HTML, CSS and Javascript

A Python-Tensorflow neural network for classifying cancer data

MATLAB implementation to segment breast lesions in ultrasound images (ICIAR 2016)

A list of web-based interactive biological data visualizations.

(No maintenance) Detect gene fusion directly from raw fastq files

Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.

CNN histopathologic tumor identifier.

Cancer Predisposition Sequencing Reporter (CPSR)

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

List of IARC bioinformatics nextflow pipelines

A basic framework for pulmonary nodule detection and characterization in CT

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Skin cancer classification using Inceptionv3

Aplicativo para o projeto "Anjos do SuperAção"

Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer

TCGA data acquisition and processing for Project Cognoma

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

It was built a web application as a step forward in building a 3D recommendation system.

SigMa is a probabilistic model for the sequential dependencies of mutation signatures

Aplicação core de gestão do programa "Anjos do Superação"

Detects hotspot regions for somatic mutations in 3D protein structures

Text mining cancer biomarkers for the CIVIC database

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data.

Functional analysis and prioritization of genesets in the context of cancer

PFA-ScanNet: Pyramidal Feature Aggregation with Synergistic Learning for Breast Cancer Metastasis Analysis

Checks if it's s**tpost saturday

R package to work with ctDNA sequencing data

Predicting Cell Health with Morphological Profiles

Training and evaluating a variational autoencoder for pan-cancer gene expression data

This project is all about a Machine Learning based Medical Test web app which makes predictions about various diseases using the concept of machine learning.

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation