Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

TCGAbiolinks

Building classifiers using cancer transcriptomes across 33 different cancer-types

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

📦 An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/

Putting machine learning in the hands of cancer biologists

Provide R access to the NCI Genomic Data Commons portal.

Make TCGA download and prepare easy!

Bioconductor package for management of multi-assay data

BioBombe: Sequentially compressed gene expression features enhances biological signatures

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

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

Interactive R package to quantify, analyse and visualise alternative splicing

TCGA data acquisition and processing for Project Cognoma

Toolbox package for organizing and working with TCGA data

A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations

Pan-cancer mycobiome atlas

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

This repo provides an exhaustive pipeline of processing TCGA whole-slide images for downstream multiple instance learning.