New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Authors
Keywords
Genome analysis, Cancer genomics, Head and neck squamous cell carcinoma, Gene expression, Carcinomas, Genetic causes of cancer, Endometrial carcinoma, Hepatocellular carcinoma
Journal
PLoS Computational Biology
Volume 15, Issue 3, Pages e1006701
Publisher
Public Library of Science (PLoS)
Online
2019-03-06
DOI
10.1371/journal.pcbi.1006701
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started