TCGAbiolinks protocols

View TCGAbiolinks computational protocol

TCGAbiolinks statistics

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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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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 in pipeline

2018
PMCID: 5869697
PMID: 29588458
DOI: 10.1038/s41598-018-23195-8

[…] benjamini-hochberg method., the mrna-seq v2 read counts produced by the cancer genome atlas (tcga) kidney renal clear cell carcinoma project were downloaded from the genomic data commons using the tcgabiolinks package (version 2.5.7). it is automatically annotated with metadata, such as patient information and the molecular subtype as determined by the original tcga analysis using hierarchical […]


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TCGAbiolinks in publications

 (23)
PMCID: 5916585
PMID: 29690901
DOI: 10.1186/s12885-018-4384-8

[…] 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” […]

PMCID: 5910392
PMID: 29679068
DOI: 10.1038/s41598-018-24769-2

[…] lung tissue samples of lung squamous cell carcinoma patients were retrieved from the publicly accessible data repository at genomic data commons data portal (https://portal.gdc.cancer.gov/) using tcgabiolinks r package. the cancer genome atlas lung squamous cell carcinoma (tcga-lusc) project entries of 44 patients containing rpm (reads per million mapped mirna reads) normalized mirna-seq data […]

PMCID: 5856809
PMID: 29549256
DOI: 10.1038/s41467-018-03494-4

[…] antibody were used as negative controls., colon cancer data were generated by the tcga research network (http://cancergenome.nih.gov/) was downloaded from the genomic data commons repository through tcgabiolinks r package., snp calls from muse, mutect, varscan and somaticsniper were combined and filtered for nonsense mutations in the gene apc. (a patient was selected if at least 1 algorithm […]

PMCID: 5852004
PMID: 29540744
DOI: 10.1038/s41598-018-22771-2

[…] 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 […]

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 […]


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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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