Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024

This repo provides the pipeline of processing TCGA whole-slide images for downstream pathology analysis.

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode

ISMB 2020: Improved survival analysis by learning shared genomic information from pan-cancer data

A unified downloader+preprocessor for cancer genomics datasets

Genomic Data Commons API wrapper

A text-based computational framework for patient -specific modeling for classification of cancers. iScience (2022).

CG - cancer genomics pipeline

The official implementations of our BIBM'24 paper: Focus on Focus: Focus-oriented Representation Learning and Multi-view Cross-modal Alignment for Glioma Grading

Classification of whole-slide images based on tumor infiltrating lymphocyte grades using image-level labels

This repository contains code for MFmap (model fidelity map), a semi-supervised generative model integrating gene expression, copy number and mutation data, matching cell lines to cancer subtypes. MFmap compresses high dimensional omics data of cell lines and bulk tumours into subtype informative low dimensional latent representations and predic…

Python implementation of the OpenGDC software /~https://github.com/cumbof/OpenGDC

Public codes for Cascaded Wx algorithm to select genes relative with patients survivals.

Use this program can let user quickly combine the miRNA/Gene expression and clinical data. Speed up the data preprocessing step.

OpenEBench TCGA benchmarking Docker declarations

Some tools to handle tcga data

A Python script to create scatter plots from files containing integrated GDC RNA expression data.

xenaPython wrapper

Python script to integrate files downloaded from the GDC server and normalized.

casskit: cancer association studies toolkit