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Cancer
56 Open Source Cancer Software Projects
Free and open source cancer code projects including engines, APIs, generators, and tools.
Deepslide
278 ⭐
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.
Pygeno
248 ⭐
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Awesome Cancer Variant Databases
192 ⭐
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Pcgr
153 ⭐
Personal Cancer Genome Reporter (PCGR)
Mutscan
109 ⭐
Detect and visualize target mutations by scanning FastQ files directly
Cognoma
91 ⭐
Putting machine learning in the hands of cancer biologists
Datamicroarray
79 ⭐
A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models.
Captk
80 ⭐
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk/
Pancancer
73 ⭐
Building classifiers using cancer transcriptomes across 33 different cancer-types
Sarek
70 ⭐
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
Genefuse
65 ⭐
Gene fusion detection and visualization
Slicerradiomics
61 ⭐
A Slicer extension to provide a GUI around pyradiomics
Genomicdatacommons
53 ⭐
Provide R access to the NCI Genomic Data Commons portal.
Civic Client
47 ⭐
Web client for CIViC: Clinical Interpretations of Variants in Cancer
2020plus
39 ⭐
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
Civic Server
35 ⭐
Backend Server for CIViC Project
Hotspot3D
35 ⭐
3D hotspot mutation proximity analysis tool
Shiny Iatlas
33 ⭐
An interactive web portal for exploring immuno-oncology data
Agfusion
31 ⭐
Python package to annotate and visualize gene fusions.
Cancer Donation Portal Python Flask App
28 ⭐
Flask App for Cancer Donation Portal using basic Python, SQLite3, HTML, CSS and Javascript
Classifying Cancer
27 ⭐
A Python-Tensorflow neural network for classifying cancer data
Bus Segmentation
29 ⭐
MATLAB implementation to segment breast lesions in ultrasound images (ICIAR 2016)
Awesome Biological Visualizations
27 ⭐
A list of web-based interactive biological data visualizations.
Fusiondirect.jl
25 ⭐
(No maintenance) Detect gene fusion directly from raw fastq files
Ci4cc Informatics Resources
23 ⭐
Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.
Histopathologic_cancer_detector
22 ⭐
CNN histopathologic tumor identifier.
Cpsr
21 ⭐
Cancer Predisposition Sequencing Reporter (CPSR)
Scarhrd
22 ⭐
Mageri
19 ⭐
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
Iarc Nf
19 ⭐
List of IARC bioinformatics nextflow pipelines
Lung Image Analysis
19 ⭐
A basic framework for pulmonary nodule detection and characterization in CT
Sigven Cacao
17 ⭐
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Skin Cancer Image Classification
16 ⭐
Skin cancer classification using Inceptionv3
Superacao App
16 ⭐
Aplicativo para o projeto "Anjos do SuperAção"
Genome Transformer
15 ⭐
Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer
Cancer Data
14 ⭐
TCGA data acquisition and processing for Project Cognoma
Imsig
15 ⭐
Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
Smartas
13 ⭐
📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.
Hyperfoods
16 ⭐
It was built a web application as a step forward in building a 3D recommendation system.
Lrgr Sigma
12 ⭐
SigMa is a probabilistic model for the sequential dependencies of mutation signatures
Superacao Core
12 ⭐
Aplicação core de gestão do programa "Anjos do Superação"
Hotmaps
13 ⭐
Detects hotspot regions for somatic mutations in 3D protein structures
Civicmine
11 ⭐
Text mining cancer biomarkers for the CIVIC database
Pdx_exomeseq
11 ⭐
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
Msk Grail Techval
11 ⭐
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
Canreg5
12 ⭐
CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data.
Oncoenrichr
11 ⭐
Functional analysis and prioritization of genesets in the context of cancer
Pfa Scannet
10 ⭐
PFA-ScanNet: Pyramidal Feature Aggregation with Synergistic Learning for Breast Cancer Metastasis Analysis
Isitsaturday
10 ⭐
Checks if it's s**tpost saturday
Ctdnatools
12 ⭐
R package to work with ctDNA sequencing data
Cell Health
10 ⭐
Predicting Cell Health with Morphological Profiles
Tybalt
114 ⭐
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Ml Mt Webapp
19 ⭐
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.
Rnaseq_titration_results
15 ⭐
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Imagemil
10 ⭐
Nf1_inactivation
10 ⭐
Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation