TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

The expanding role of primary care in cancer control

(2015) Greg Rubin et al.   LANCET ONCOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

(2014) Caleb F. Davis et al.   CANCER CELL

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

(2014) Nishant Agrawal et al.   CELL

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

TCGA-Assembler: open-source software for retrieving and processing TCGA data

(2014) Yitan Zhu et al.   NATURE METHODS

The UCSC Cancer Genomics Browser: update 2015

(2014) Mary Goldman et al.   NUCLEIC ACIDS RESEARCH

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data

(2014) Mehmet Kemal Samur   PLoS One

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

canEvolve: A Web Portal for Integrative Oncogenomics

(2013) Mehmet Kemal Samur et al.   PLoS One

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Making sense of cancer genomic data

(2011) Lynda Chin et al.   GENES & DEVELOPMENT

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

(2011) T. Hinoue et al.   GENOME RESEARCH

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE