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

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

Python script to create a heatmap based on correlations in GDC expression data of PTEN with other genes.

xenaPython wrapper

Some tools to handle tcga data

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

TCGA Cancer Detection (for MuG/VRE OpenEBench installation)

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

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

Genomic Data Commons API wrapper

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

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…

OpenEBench TCGA benchmarking Docker declarations

CG - cancer genomics pipeline

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

casskit: cancer association studies toolkit

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

The Cancer Genome Atlas (TCGA), a cancer genomics reference program, has molecularly characterized more than 20,000 primary cancer samples and paired normal samples covering 33 types of cancer. This joint effort between the NCI and the National Human Genome Research Institute began in 2006.

A unified downloader+preprocessor for cancer genomics datasets