GEOquery protocols

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GEOquery specifications

Information


Unique identifier OMICS_01972
Name GEOquery
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.48.0
Stability Stable
Requirements
limma, methods, BiocGenerics, Biobase, testthat, dplyr, rmarkdown, knitr, readr, httr, xml2, tidyr, magrittr, covr
Maintained Yes

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Publication for GEOquery

GEOquery in pipelines

 (11)
2018
PMCID: 5822876
PMID: 29577053
DOI: 10.1155/2018/9412387

[…] and the list of gses is shown in supplementary table . gse2053 is the only dataset generated from human ra sample assays. datasets from other species or other tissues were filtered out. the geoquery and limma r packages were then used to screen the differentially expressed genes in ra (ra-degs). functional enrichment analyses conducted by david and genecards [, ], which are based […]

2017
PMCID: 5400636
PMID: 28423538
DOI: 10.18632/oncotarget.15749

[…] significant unless otherwise mentioned. a cutoff value of fdr<0.1 was used for multiple comparisons. r packages ggplot2, venndiagram, and pheatmap were used for data visualization; mygene, geoquery and gostats were used for gene symbol mapping and go enrichment. r packages survival and mass were used for survival analysis., we thank dr. kimberly glass, the author of panda, for her help […]

2017
PMCID: 5457141
PMID: 28489004
DOI: 10.7554/eLife.23253.044

[…] for p value estimated with 1000 permutations. results of gsea are listed in in ., microarray data of time course study of erk activation () were retrieved from the gene expression omnibus using geoquery () under the accession number gse59755. technical sources of variation were removed with combat function of the sva package (). differentially expressed genes with two fold changes […]

2016
PMCID: 4865003
PMID: 27169379
DOI: 10.1186/s12864-016-2650-1

[…] employed. the data set generated 90 gene expression profiles containing 84,246 probe sets using the affymetrix chip platform. combined expression profiles were extracted and normalized using the geoquery [] package. co-expression correlation between lncrna probes and non-lncrna probes was then calculated using pearson correlation with r2 ≥ 0.85. the normalized expression data from lncrnas […]

2016
PMCID: 5064772
PMID: 27737314
DOI: 10.1590/1414-431X20164897

[…] the calculation of expression values, the raw data of each chip were first normalized using the geoquery package (version 2.34.0, available at http://www.bioconductor.org/packages/release/bioc/html/geoquery.html) () in r language. after, the expression data were log2 transformed, and a linear regression model was constructed to compare the gene expression in dcm and control samples. then, […]


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GEOquery in publications

 (140)
PMCID: 5935809
PMID: 29203636
DOI: 10.1302/2046-3758.612.BJR-2017-0102.R1

[…] of osteoporosis., the two microarray data sets (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse56815 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse56814) were downloaded using the geoquery package with r version (the r foundation for statistical computing, vienna, austria) from the gene expression omnibus (geo) database. these two microarray data sets were from the blood […]

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

[…] 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”, and subsequent analysis was performed on the above two probes. the expression of cd274 in the samples […]

PMCID: 5903354
PMID: 29664470
DOI: 10.1038/sdata.2018.66

[…] review board (e 14522)., for each dataset, we wrote custom r scripts that download, parse, and reformat the clinical annotations. initially, these scripts retrieve data from geo using the geoquery package. next they generate a tab-delimited text file for each dataset that contains all available clinical annotations, except those with identical values for all samples (for example, […]

PMCID: 5899355
PMID: 29653596
DOI: 10.1186/s12920-018-0357-7

[…] in table .table 1pd parkinson’s disease, hc healthy control, pd parkinson’s disease, hc healthy control, searches were executed up to august 2017., geo2r is an interactive web tool that is based on geoquery and limma r packages from the bioconductor project that is used to identify degs by comparing different groups of geo series samples []. in this study, each individual dataset was processed […]

PMCID: 5883274
PMID: 29614959
DOI: 10.1186/s12864-018-4578-0

[…] oligo array hybridizations, gene expression normalization, and partial outcomes are available for nxiits [], ra [], and area x []. for our present analysis of these oligo arrays we used the geoquery and limma r packages (ncbi gene expression omnibus; [] with the benjamini & hochberg false discovery rate method to identify differentially expressed oligos from the user-supplied […]


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GEOquery institution(s)
Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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