GEOmetadb statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool GEOmetadb
info

Tool usage distribution map

This map represents all the scientific publications referring to GEOmetadb per scientific context
info info

Associated diseases

This word cloud represents GEOmetadb usage per disease context
info

Popular tool citations

chevron_left Gene expression data mining chevron_right
Want to access the full stats & trends on this tool?

Protocols

GEOmetadb specifications

Information


Unique identifier OMICS_14416
Name GEOmetadb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Yidong Chen

Information


Unique identifier OMICS_14416
Name GEOmetadb
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yidong Chen

Publication for GEOmetadb

GEOmetadb citations

 (18)
library_books

ALE: automated label extraction from GEO metadata

2017
BMC Bioinformatics
PMCID: 5751806
PMID: 29297276
DOI: 10.1186/s12859-017-1888-1

[…] e, and normalized between arrays by quantile normalization. Imputation of missing values was done using k-nearest neighbors with k = 5. Metadata text for the downloaded GEO data was obtained from the GEOmetadb package [] which contains several key fields with the label and experiment types of interest, such as “Title”, “Source Name” (usually referring to the tissue or cell line), “Organism”, “Desc […]

library_books

Wide Open: Accelerating public data release by automating detection of overdue datasets

2017
PLoS Biol
PMCID: 5464523
PMID: 28594819
DOI: 10.1371/journal.pbio.2002477

[…] d Archive (SRA). To scan PubMed text for accession numbers, Wide-Open uses the regular expression GSE[0–9]+ for GEO, and SRX[0–9]+ for SRA. For each candidate accession number, Wide-Open first checks GEOmetadb [] for GEO, and SRAdb [] for SRA. A hit means that the dataset has been released. If not, Wide-Open calls the web APIs for GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= […]

call_split

Imputing gene expression to maximize platform compatibility

2016
Bioinformatics
PMCID: 5408923
PMID: 27797771
DOI: 10.1093/bioinformatics/btw664
call_split See protocol

[…] r purposes, and only GSEs containing at least three valid samples were retained. In total, 97 049 microarray CEL files, coming from 2753 accepted GSEs, were downloaded. The R packages GEOquery () and GEOmetadb () were used to perform the above tasks.The CEL files within each GSE were processed using robust multi-array average (RMA) (; ). Technical bias correction was done using the R package bias […]

call_split

Microarray Data Processing Techniques for Genome Scale Network Inference from Large Public Repositories

2016
Microarrays
PMCID: 5040970
PMID: 27657141
DOI: 10.3390/microarrays5030023
call_split See protocol

[…] h of these databases stores the experiment metadata in a different format, and therefore, we used different methods to collect data files from the corresponding websites. In case of GEO, we used the “GEOmetadb” Bioconductor library [] to extract the description and experiment metadata, and used this metadata to download the corresponding microarray data files (CEL files) from National Center for B […]

library_books

Absence of genomic hypomethylation or regulation of cytosine modifying enzymes with aging in male and female mice

2016
PMCID: 4942942
PMID: 27413395
DOI: 10.1186/s13072-016-0080-6

[…] data were obtained from NCBI’s GEO database of publicly available microarray experiments and collapsed to genes by max mean using the probe–gene mappings provided by the AILUN database []. The SQLite GEOmetadb database containing descriptions of the experiments was downloaded, and the age and tissue of each sample was extracted using text mining. The following random-effects linear model was fit t […]

call_split

A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research

2016
F1000Res
PMCID: 4856112
PMID: 27158452
DOI: 10.5256/f1000research.8800.r12768
call_split See protocol

[…] Potentially relevant datasets deposited in GEO were identified using an advanced query based on the Bioconductor package GEOmetadb and the SQLite database that captures detailed information on the GEO data structure; https://www.bioconductor.org/packages/release/bioc/html/GEOmetadb.html . The search query was designed t […]


Want to access the full list of citations?
GEOmetadb institution(s)
Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Advanced Biomedical Computing Center, National Cancer Institute-Frederick/SAIC-Frederick Inc, Frederick, MD, USA
GEOmetadb funding source(s)
This work was supported by Intramural Research Program of the NIH, National Cancer Institute, Bethesda, USA.

GEOmetadb reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GEOmetadb