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 Slicer extension to provide a GUI around pyradiomics

Opensource radiation treatment planning system in Python [AAPM'23]

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

Python package to annotate and visualize gene fusions.

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

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

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

The official implementation of GPFM

Multi-task deep learning framework for multi-omics data analysis

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

A Python-Tensorflow neural network for classifying cancer data

MADELEINE: multi-stain slide representation learning (ECCV'24)

Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets. KG4SL is the first graph neural network (GNN)-based model that uses knowledge graph for SL prediction.

PFA-ScanNet: Pyramidal Feature Aggregation With Synergistic Learning for Breast Cancer Metastasis Analysis (Architecture Only Pytorch Implementation).

Text mining cancer biomarkers for the CIVIC database

Pulmonary nodules computer-aided diagnosis demo system.

Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)

Patient-Specific Modeling in Python