Package: GEOquery 2.73.0

Sean Davis

GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Authors:Sean Davis [aut, cre]

GEOquery_2.73.0.tar.gz
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GEOquery.pdf |GEOquery.html✨
GEOquery/json (API)
NEWS

# Install 'GEOquery' in R:

install.packages('GEOquery', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/seandavi/geoquery/issues

On BioConductor:GEOquery-2.73.0(bioc 3.20)GEOquery-2.72.0(bioc 3.19)

bioconductor-package

17 exports 5.18 score 41 dependencies 57 dependents 328 mentions

Last updated 2 months agofrom:1e54ba1f20

Exports:Accession Columns dataTable GDS2eSet GDS2MA getGEO getGEOfile getGEOSuppFiles getGSEDataTables GPL GPLList GSMList gunzip Meta parseGEO show Table

Dependencies:Biobase BiocGenerics bit bit64 cli clipr cpp11 crayon curl data.table dplyr fansi generics glue hms lifecycle limma magrittr pillar pkgconfig prettyunits progress purrr R.methodsS3 R.oo R.utils R6 readr rlang statmod stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs vroom withr xml2

Using the GEOquery Package

Sean Davis

Rendered fromGEOquery.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2022-05-11
Started: 2014-09-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert a GDS data structure to a BioConductor data structure	coercion GDS2eSet GDS2MA
Class "GDS"	GDS-class
Generic functions for GEOquery	Accession Columns dataTable GEOData-accessors GPLList GSMList Meta Table
Class "GEOData"	Accession,GEOData-method Columns,GEOData-method dataTable,GEOData-method GEOData-class Meta,GEOData-method show,GEOData-method Table,GEOData-method
Class "GEODataTable"	Accession,GEODataTable-method Columns,GEODataTable-method dataTable,GEODataTable-method GEODataTable-class Meta,GEODataTable-method show,GEODataTable-method Table,GEODataTable-method
get a directory listing from NCBI GEO	getDirListing
Get a GEO object from NCBI or file	getGEO
Download a file from GEO soft file to the local machine	getGEOfile
Get Supplemental Files from GEO	getGEOSuppFiles
Get GSE data tables from GEO into R data structures.	getGSEDataTables
Class "GPL"	GPL GPL,GDS-method GPL-class
Class "GSE"	GPLList,GSE-method GSE-class GSMList,GSE-method Meta,GSE-method
Class "GSM"	GSM-class
Gunzip a file	gunzip
Parse GEO text	parseGDS parseGEO parseGPL parseGSE parseGSM