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

TCGAbiolinks

📦R包：Make TCGA download and prepare easy!

📦 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/

Provide R access to the NCI Genomic Data Commons portal.

Bioconductor package for management of multi-assay data

Interactive R package to quantify, analyse and visualise alternative splicing

Toolbox package for organizing and working with TCGA data

A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research

The pipeline to produce TCGA data as MultiAssayExperiment objects

Batch-harmonized ML framework for cross-cohort RNA biomarker discovery in pancreatic adenocarcinoma — bioRxiv 2025 (doi:10.1101/2025.11.14.688421)

DEEPEST-Fusion is a fusion detection algorithm specially designed for screening massive cancer sequencing databases

Supplementary Material of manuscript, and Cutoff Finding R script

Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data

Simulation of interactions miRNA:Competing Targets

Example data to TCGAWorkflow

An R package for TCGA clinical data mining

Resolving the GPRC5A prognostic paradox in PDAC: subtype stratification, treatment deconfounding, proteomics, AlphaFold2, ML (R) — manuscript in prep

HNSCC survival analysis

Benchmark survival ML models against a multimodal TCGA dataset