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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

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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

 (11)
library_books

Imputing gene expression to maximize platform compatibility

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

[…] 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 […]

library_books

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

2016
Microarrays
PMCID: 5040970
PMID: 27657141
DOI: 10.3390/microarrays5030023

[…] 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 […]

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

[…] 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 […]

library_books

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

[…] immunobiology, representing a total of 4,516 transcriptome profiles., 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 […]

library_books

A curated transcriptome dataset collection to investigate the functional programming of human hematopoietic cells in early life

2016
F1000Res
PMCID: 4916988
PMID: 27347375
DOI: 10.5256/f1000research.9008.r13168

[…] stages. this process involved reading through the descriptions and examining the list of available samples and their annotations. for the filtering of the dataset list, the bioconductor package geometadb, version 1.30.0, and its sqlite database was used to capture detailed information on selected geo datasets in a single table ( […]

library_books

A curated transcriptome dataset collection to investigate the immunobiology of HIV infection

2016
F1000Res
PMCID: 4838008
PMID: 27134731
DOI: 10.5256/f1000research.8824.r12874

[…] and relevant literature, study design, and detailed sample information., potentially relevant datasets deposited in geo were identified using an advanced query based on the bioconductor package geometadb, version 1.30.0, and on the sqlite database that captures detailed information on geo data structure ( https://www.bioconductor.org/packages/release/bioc/html/geometadb.html) . the search […]


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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.

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