Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

TCGAbiolinks

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

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

Cancer-dedicated gene set interpretation

TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/

Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data

Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment

Demographic bias in misdiagnosis by computational pathology models - Nature Medicine

Bioinformatics Pipeline

A database for microRNA-gene/protein expression correlation in cancer.

Computational approach to identify Survival associated Pairwise Gene Expression states.

GNU Make-driven workflow to download TCGA data via the TCGAbiolinks package

a neural network-based feature selection algorithm for next-generation sequencing data

Tumor2Graph: a novel Overall-Tumor-Profile-derived virtual graph deep learning for predicting tumor typing and subtyping.

This repo stores codes for the analysis of tasrkleat results on TCGA RNA-Seq dataa

TCGA hg19 and hg38 data downloader.

BSc thesis: "Convolutional Neural Networks and their Application in Cancer Diagnosis based on RNA-Sequencing"

Examples on processing and working with TCGA mutation and RNA-Seq data