TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
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Cites background or methods from "TCGAbiolinks: an R/Bioconductor pac..."
...PanCancer TCGA RNA sequence level 3 normalized data were downloaded from the GDC Data Portal using TCGAbiolinks functions GDCquery, GDCdownload and GDCprepare importing into R (http://www.r-project.org) for further analysis (Colaprico et al., 2016)....
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...4.3) Colaprico et al., 2016 http://bioconductor.org/packages/release/bioc/html/ TCGAbiolinks.html ELMER (v1....
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...…available at TCGAbiolinks Cell 173, 338–354.e1–e5, April 5, 2018 e3 package (http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html) (Colaprico et al., 2016; Silva et al., 2017), through the function ‘‘PanCancerAtlas_subtypes(),’’ which provides full access to the curated matrix…...
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...Level 3 data were downloaded from TCGA Data Portal using TCGAbiolinks functions GDCquery, GDCdownload and GDCprepare importing into R (http://www.r-project.org) for further analysis (Colaprico et al., 2016)....
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...…33 mRNA expression signatures (one for each cancer type) by applying a differential expression analysis to samples with highmRNAsi and lowmRNAsi, using the function TCGAanalyze_DEA from the the R/Bioconductor package TCGAbiolinks version 2.5.9 (Colaprico et al., 2016), carrying edgeR pipeline....
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831 citations
References
83,420 citations
"TCGAbiolinks: an R/Bioconductor pac..." refers methods in this paper
...The P-values generated from the analysis are sorted in ascending order and corrected using the Benjamini & Hochberg procedure for multiple testing correction (30)....
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29,413 citations
"TCGAbiolinks: an R/Bioconductor pac..." refers methods in this paper
...In particular, we used the edgeR package from Bioconductor, which uses the quantile-adjusted conditional maximum likelihood (qCML) method for experiments with a single factor to detect differentially expressed genes (DEGs) (27)....
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...Specifically, the objects are summarized in a ‘SummarizedExperiment’ object (3) to allow easy integration with other Bioconductor packages, such as GRanges (25), IRanges (25), limma (26) and edgeR (27)....
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22,147 citations
"TCGAbiolinks: an R/Bioconductor pac..." refers methods in this paper
...Specifically, the objects are summarized in a ‘SummarizedExperiment’ object (3) to allow easy integration with other Bioconductor packages, such as GRanges (25), IRanges (25), limma (26) and edgeR (27)....
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12,142 citations
"TCGAbiolinks: an R/Bioconductor pac..." refers background or methods in this paper
...TCGAbiolinks is an R package, which is licensed under the General Public License (GPLv3), and is freely available through the Bioconductor repository (21)....
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...The Bioconductor project ensures high-quality, well-documented and interoperable software and the possibility of integration with hundreds of available packages within R (21)....
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...Although RTCGAToolbox can download and analyze Firehose-generated data, neither tool can provide the downloaded data as a ‘SummarizedExperiment’ object, which is critical for allowing the full integration and use of other popular Bioconductor packages, an integral aspect of Bioconductor (21,22)....
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10,947 citations
Additional excerpts
...org/), RTCGAToolbox (19) and cBioPortal (20)....
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