DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Personal Cancer Genome Reporter (PCGR)

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

Utilities to download and load an MRI brain tumor dataset with Python, providing 2D slices, tumor masks and tumor classes.

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

Sturgeon is a CNS neural network classifier

a PyQt5 Implementation

Extract and evaluate radiomics for liver cancer tumors from DICOM segmentation masks. Using SimpleITK, PyRadiomics and PyDicom.

🦀 Tumor growth simulation in C++/R

Code, data and model for Pérez-García et al. 2021, "A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections"

3D Slicer plugin for automatic segmentation and generation of standardized clinical reports for the most common brain tumors, using MRI volumes

CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data

Clinical oncology tumor board decision support system made by the Decider project.

Deep Learning for Automatic Differential Diagnosis of Primary Central Nervous System Lymphoma and Glioblastoma: Multi-parametric MRI based Convolutional Neural Network Model

This repository covers a brain scan tumor classification project for the University of Washington DATA 515 course. In our project we train a CNN to predict if a MRI scan (.jpg, .png, .jpeg) is tumorous or not.

Tool to estimate purity of tumor samples exploiting DNA Methylation data

A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research

🐳 Dockerized WES pipeline for variants identification in mathced tumor-normal samples

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