New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

N -glycan signatures identified in tumor interstitial fluid and serum of breast cancer patients: association with tumor biology and clinical outcome

(2018) Thilde Terkelsen et al.   Molecular Oncology

Unifying cancer and normal RNA sequencing data from different sources

(2018) Qingguo Wang et al.   Scientific Data

Reproducible RNA-seq analysis using recount2

(2017) Leonardo Collado-Torres et al.   NATURE BIOTECHNOLOGY

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

(2017) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

Web-TCGA: an online platform for integrated analysis of molecular cancer data sets

(2016) Mario Deng et al.   BMC BIOINFORMATICS

A Case for Data Commons: Toward Data Science as a Service

(2016) Robert L. Grossman et al.   COMPUTING IN SCIENCE & ENGINEERING

Facilitating a culture of responsible and effective sharing of cancer genome data

(2016) Lillian L Siu et al.   NATURE MEDICINE

CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms

(2016) George S. Krasnov et al.   NUCLEIC ACIDS RESEARCH

TCGA Expedition: A Data Acquisition and Management System for TCGA Data

(2016) Uma R. Chandran et al.   PLoS One

Cytokine profiling of tumor interstitial fluid of the breast and its relationship with lymphocyte infiltration and clinicopathological characteristics

(2016) Jaime A. Espinoza et al.   OncoImmunology

The Genotype-Tissue Expression (GTEx) Project

(2015) Latarsha J. Carithers et al.   BIOPRESERVATION AND BIOBANKING

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

TCGASpliceSeq a compendium of alternative mRNA splicing in cancer

(2015) Michael Ryan et al.   NUCLEIC ACIDS RESEARCH

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

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

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

(2015) Katarzyna Tomczak et al.   Wspolczesna Onkologia-Contemporary Oncology

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

The Genotype-Tissue Expression (GTEx) Project

(2015) Latarsha J. Carithers et al.   Biopreservation and Biobanking

Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us?

(2015) Veronique G. LeBlanc et al.   Cancers

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data

(2014) Mehmet Kemal Samur   PLoS One

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

RNA-Seq: revelation of the messengers

(2013) Marcel C. Van Verk et al.   TRENDS IN PLANT SCIENCE

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser

(2013) Melissa S. Cline et al.   Scientific Reports

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

The Pediatric Cancer Genome Project

(2012) James R Downing et al.   NATURE GENETICS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

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

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

Involvement of Members of the Cadherin Superfamily in Cancer

(2009) G. Berx et al.   Cold Spring Harbor Perspectives in Biology

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The tumor microenvironment and its role in promoting tumor growth

(2008) T L Whiteside   ONCOGENE