GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

By Sean Davis, Paul S. Meltzer. Bioinform., 2007

2,790 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c6480aecd32cff4ebbd9d12e0c351249cd76a760

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Citations in the corpus

NCBI GEO: archive for functional genomics data sets—10 years on (2010, methodology): “(I) Bioconductor GEOquery package published, allowing GEO data to be imported into R environment (22).”
NCBI GEO: archive for high-throughput functional genomic data (2008, methodology): “For users who need to perform more robust analyses, all GEO data are available for bulk download via anonymous FTP at ftp://ftp.ncbi.nih.gov/pub/geo/ DATA/ and can be imported into external third-party software applications, e.g. the freely available GEOquery package for BioConductor (12).”
CuMiDa: An Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research (2019, methodology): “…sets [GEO Series (GSEs)], data of multiple subtypes of colorectal , gastric , pancreatic , liver , bladder , lung , throat , renal , brain , prostate , ovary , leukemia , and breast cancers were downloaded from GEO database using the GEOquery package (Davis and Meltzer, 2007) for the R platform.”
Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines (2014, methodology): “Davis S, Meltzer PS: GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.”
Massive mining of publicly available RNA-seq data from human and mouse (2017, methodology): “All available SRA files are identified by downloading the GEO series (GSE) and GEO samples (GSM and SRA information) using the GEOquery Bioconductor package (19).”
The Gene Expression Omnibus database (2016, methodology): “It uses a Web-based program that employs the Bioconductor [14] packages GEOQuery [15] and limma [16] in R, with the Benjamini–Hochberg false-discovery rate method [17] for multiple-testing correction as its default method.”
Global Mapping of Small RNA-Target Interactions in Bacteria (2016, methodology): “, 2015) with the GEOquery package (Davis and Meltzer, 2007) were used to assess the log2 fold change in expression of all genes measured in each of the experiments.”
Multiple testing with the structure‐adaptive Benjamini–Hochberg algorithm (2016, methodology): “In this sense, this version of our method can be viewed as a relaxation of the ordered testing methods of Grazier G’Sell et al. (2015), Barber and Candès (2015) and Li and Barber (2017).”
NCBI GEO: archive for functional genomics data sets—update (2012, methodology): “These parameters are passed to the back end where a ‘GEOquery’ (14) call loads the corresponding SeriesMatrix file and platform annotation files via FTP and returns the ExpressionSet object and contrasts, which are input for two R scripts, ‘boxplot’, which draws a boxplot of the distribution of expr”