TCGAbiolinks statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TCGAbiolinks
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Protocols

TCGAbiolinks specifications

Information


Unique identifier OMICS_10961
Name TCGAbiolinks
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.8.4
Stability Stable
Requirements
limma, methods, stats, plyr, RColorBrewer, parallel, grid, graphics, Biobase, IRanges, GenomicRanges, utils, testthat, S4Vectors, GenomeInfoDb, BiocStyle, grDevices, tools, dplyr, ggplot2, affy, biomaRt, GenomicFeatures, scales, data.table, rmarkdown, knitr, genefilter, survival, R(>=3.2), readr, R.utils, igraph, edgeR(>=3.0.0), xml2, doParallel, sva, gridExtra, png, devtools, matlab, clusterProfiler, parmigene, tibble, minet, circlize, downloader(>=0.4), survminer, XML(>=3.98.0), EDASeq(>=2.0.0), jsonlite(>=1.0.0), ggthemes, stringr(>=1.0.0), rvest(>=0.3.0), selectr, ComplexHeatmap(>=1.10.2), SummarizedExperiment(>=1.4.0), ConsensusClusterPlus, httr(>=1.2.1), ggrepel(>=0.6.3), maftools, c3net, dnet, pathview, supraHex
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Antonio Colaprico
  • person_outline Luigi Cerulo
  • person_outline Houtan Noushmehr
  • person_outline Tiago Chedraoui Silva

Additional information


GUI version: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI Demo: https://tcgabiolinksgui.shinyapps.io/demo/

Publications for TCGAbiolinks

TCGAbiolinks citations

 (17)
library_books

CXCL9/10/11, a regulator of PD L1 expression in gastric cancer

2018
BMC Cancer
PMCID: 5916585
PMID: 29690901
DOI: 10.1186/s12885-018-4384-8

[…] pore patient cohort []. Dataset GSE62254 contained surgically resected 300 GC samples with complete data from the Korean patient cohort [].The TCGA data was preprocessed according to the Bioconductor/TCGABiolinks function package flow. The gene expression profile data were extracted using the Bioconductor/GEOquery function package. Gene CD274 corresponds to two probes, “223834_at” and “227458_at”, […]

library_books

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal

2018
Cell
PMCID: 5927631
PMID: 29656891
DOI: 10.1016/j.cell.2018.02.020

[…] hat are present on the duplicated arm of chromosome 5q;There are any significantly differentially expressed genes in the region of the unbalanced t(3;5) translocation.Data was downloaded in R via the TCGABiolinks package from Bioconductor. Subsequent analysis was carried out using the R package edgeR.We initially removed all samples with fewer than a total of 20 million reads, and all genes that d […]

call_split

Alpha oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A

2018
Sci Rep
PMCID: 5852004
PMID: 29540744
DOI: 10.1038/s41598-018-22771-2
call_split See protocol

[…] cording to standards outlined by minfi. Annotations were added using IlluminaMethylationManifest, a class built within the minfi package. Volcano plots were constructed using the Biconductor package, TCGAbiolinks. Heatmaps were created using the Bioconductor package, ComplexHeatmap. Differentially methylated genes (DMGs) were identified using a simple T-test comparing treated and un-treated groups […]

library_books

NFkB hyperactivation causes invasion of esophageal squamous cell carcinoma with EGFR overexpression and p120 catenin down regulation

2018
Oncotarget
PMCID: 5834278
PMID: 29541406
DOI: 10.18632/oncotarget.24358

[…] Normalized RNA sequencing expression data from 182 esophageal squamous cell carcinomas were downloaded from The Cancer Genome Atlas (TCGA) Data Commons (https://portal.gdc.cancer.gov/) using the TCGAbiolinks package [] using R version 3.3.1 []. Expression data were log2 transformed. Based on review of histograms, cases were considered p120ctn-high or p120ctn-low if levels of p120ctn were in t […]

call_split

IFNγ induces PD L1 overexpression by JAK2/STAT1/IRF 1 signaling in EBV positive gastric carcinoma

2017
Sci Rep
PMCID: 5736657
PMID: 29259270
DOI: 10.1038/s41598-017-18132-0
call_split See protocol

[…] GSEA was performed using Bioconductor R packages, including TCGAbiolinks and Ensemble of GSEA (EGSEA),. RNA-sequencing data were downloaded and preprocessed using TCGAbiolinks and annotated with Entrez ID. Differentially expressed genes between EBV (+) and EBV […]

library_books

Comparing the genomes of cutaneous melanoma tumors to commercially available cell lines

2017
Oncotarget
PMCID: 5777739
PMID: 29383127
DOI: 10.18632/oncotarget.22928

[…] Data processing and statistical analysis was carried out using Linux shell scripting and R version 3.3.2 []. Bioconductor packages were applied as necessary including CNTools, biomaRt, TCGAbiolinks, ComplexHeatmap, maftools, cometExactTest and RColorBrewer []. Other R packages were applied to create plots and make calculations including dplyr, ggplot2, reshape2, and ggsignif. Hierar […]


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TCGAbiolinks institution(s)
Department of Science and Technology, University of Sannio, Benevento, Italy; BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino (AV) Italy; Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
TCGAbiolinks funding source(s)
Supported by a research project funded by MiUR (Ministero dell’Università e della Ricerca) under grant FIRB2012-RBFR12QW4I.

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