GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

Keywords

bioconductor bioinformatics data-science genomics ncbi-geo r rstats

Keywords from Contributors

bioconductor-packages mass-spectrometry metabolomics gene proteomics peak-detection feature-detection hdf5 looking-for-maintainer rhdf5

Last synced: 4 months ago · JSON representation ·

Repository

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

Basic Info

Host: GitHub
Owner: seandavi
License: other
Language: R
Default Branch: devel
Homepage: http://seandavi.github.io/GEOquery/
Size: 20.3 MB

Statistics

Stars: 98
Watchers: 5
Forks: 36
Open Issues: 25
Releases: 0

Topics

bioconductor bioinformatics data-science genomics ncbi-geo r rstats

Created over 12 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog License Code of conduct Citation

README.md

Status

Installation

To install from Bioconductor, use the following code:

```

if needed, install BiocManager

install.packages("BiocManager")

install GEOquery

BiocManager::install("GEOquery") ```

To install directly from github:

BiocManager::install('seandavi/GEOquery')

Usage

See the full vignette in rmarkdown or visit Bioconductor for details:

How to contribute

Contributions to GEOquery development can be submitted as a pull request or a feature request issue. We recommend following the Bioconductor coding standards where possible.

Owner

Name: Sean Davis
Login: seandavi
Kind: user
Location: Bethesda, MD, 20892, USA
Company: National Cancer Institute, National Institutes of Health

Website: https://seandavi.github.io/
Repositories: 87
Profile: https://github.com/seandavi

- Pediatric oncologist - Cancer researcher - Data scientist - Community organizer

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "GEOquery" in publications use:'
type: software
license: MIT
title: 'GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)'
version: 2.73.5
doi: 10.1093/bioinformatics/btm254
identifiers:
- type: url
  value: http://seandavi.github.io/GEOquery
- type: url
  value: http://seandavi.github.io/GEOquery/
abstract: 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:
- family-names: Davis
  given-names: Sean
  email: seandavi@gmail.com
  orcid: https://orcid.org/0000-0002-8991-6458
preferred-citation:
  type: article
  title: 'GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor'
  authors:
  - family-names: Davis
    given-names: Sean
    email: seandavi@gmail.com
    orcid: https://orcid.org/0000-0002-8991-6458
  - family-names: Meltzer
    given-names: Paul
  journal: Bioinformatics
  year: '2007'
  volume: '14'
  doi: 10.1093/bioinformatics/btm254
  start: '1846'
  end: '1847'
repository: https://bioconductor.org/
repository-code: https://github.com/seandavi/GEOquery/issues/new
url: https://github.com/seandavi/GEOquery
date-released: '2024-10-28'
contact:
- family-names: Davis
  given-names: Sean
  email: seandavi@gmail.com
  orcid: https://orcid.org/0000-0002-8991-6458
references:
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: Biobase
  abstract: 'Biobase: Biobase: Base functions for Bioconductor'
  notes: Depends
  url: https://bioconductor.org/packages/Biobase
  repository: https://bioconductor.org/
  authors:
  - family-names: Gentleman
    given-names: R.
  - family-names: Carey
    given-names: V.
  - family-names: Morgan
    given-names: M.
  - family-names: Falcon
    given-names: S.
  year: '2024'
  doi: 10.18129/B9.bioc.Biobase
- type: software
  title: readr
  abstract: 'readr: Read Rectangular Text Data'
  notes: Imports
  url: https://readr.tidyverse.org
  repository: https://CRAN.R-project.org/package=readr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Hester
    given-names: Jim
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2024'
  doi: 10.32614/CRAN.package.readr
  version: '>= 1.3.1'
- type: software
  title: xml2
  abstract: 'xml2: Parse XML'
  notes: Imports
  url: https://xml2.r-lib.org/
  repository: https://CRAN.R-project.org/package=xml2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Hester
    given-names: Jim
  - family-names: Ooms
    given-names: Jeroen
  year: '2024'
  doi: 10.32614/CRAN.package.xml2
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2024'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  url: https://r-datatable.com
  repository: https://CRAN.R-project.org/package=data.table
  authors:
  - family-names: Barrett
    given-names: Tyson
    email: t.barrett88@gmail.com
  - family-names: Dowle
    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  - family-names: Gorecki
    given-names: Jan
  - family-names: Chirico
    given-names: Michael
  - family-names: Hocking
    given-names: Toby
    orcid: https://orcid.org/0000-0002-3146-0865
  year: '2024'
  doi: 10.32614/CRAN.package.data.table
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2024'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
  doi: 10.32614/CRAN.package.magrittr
- type: software
  title: limma
  abstract: 'limma: Linear Models for Microarray Data'
  notes: Imports
  url: https://bioinf.wehi.edu.au/limma/
  repository: https://bioconductor.org/
  authors:
  - family-names: Smyth
    given-names: Gordon
  - family-names: Hu
    given-names: Yifang
  - family-names: Ritchie
    given-names: Matthew
  - family-names: Silver
    given-names: Jeremy
  - family-names: Wettenhall
    given-names: James
  - family-names: McCarthy
    given-names: Davis
  - family-names: Wu
    given-names: Di
  - family-names: Shi
    given-names: Wei
  - family-names: Phipson
    given-names: Belinda
  - family-names: Lun
    given-names: Aaron
  - family-names: Thorne
    given-names: Natalie
  - family-names: Oshlack
    given-names: Alicia
  - family-names: Graaf
    given-names: Carolyn
    name-particle: de
  - family-names: Chen
    given-names: Yunshun
  - family-names: Giner
    given-names: Goknur
  - family-names: Langaas
    given-names: Mette
  - family-names: Ferkingstad
    given-names: Egil
  - family-names: Davy
    given-names: Marcus
  - family-names: Pepin
    given-names: Francois
  - family-names: Choi
    given-names: Dongseok
  - family-names: Law
    given-names: Charity
  - family-names: Li
    given-names: Mengbo
  year: '2024'
  doi: 10.18129/B9.bioc.limma
- type: software
  title: curl
  abstract: 'curl: A Modern and Flexible Web Client for R'
  notes: Imports
  url: https://jeroen.r-universe.dev/curl
  repository: https://CRAN.R-project.org/package=curl
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2024'
  doi: 10.32614/CRAN.package.curl
- type: software
  title: rentrez
  abstract: 'rentrez: ''Entrez'' in R'
  notes: Imports
  url: https://docs.ropensci.org/rentrez/
  repository: https://CRAN.R-project.org/package=rentrez
  authors:
  - family-names: Winter
    given-names: David
    email: david.winter@gmail.com
    orcid: https://orcid.org/0000-0002-6165-0029
  year: '2024'
  doi: 10.32614/CRAN.package.rentrez
- type: software
  title: R.utils
  abstract: 'R.utils: Various Programming Utilities'
  notes: Imports
  url: https://henrikbengtsson.github.io/R.utils/
  repository: https://CRAN.R-project.org/package=R.utils
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2024'
  doi: 10.32614/CRAN.package.R.utils
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  url: https://stringr.tidyverse.org
  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.stringr
- type: software
  title: SummarizedExperiment
  abstract: 'SummarizedExperiment: SummarizedExperiment container'
  notes: Imports
  url: https://bioconductor.org/packages/SummarizedExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Hester
    given-names: Jim
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  year: '2024'
  doi: 10.18129/B9.bioc.SummarizedExperiment
- type: software
  title: S4Vectors
  abstract: 'S4Vectors: Foundation of vector-like and list-like containers in Bioconductor'
  notes: Imports
  url: https://bioconductor.org/packages/S4Vectors
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  - family-names: Lawrence
    given-names: Michael
  - family-names: Aboyoun
    given-names: Patrick
  year: '2024'
  doi: 10.18129/B9.bioc.S4Vectors
- type: software
  title: rvest
  abstract: 'rvest: Easily Harvest (Scrape) Web Pages'
  notes: Imports
  url: https://rvest.tidyverse.org/
  repository: https://CRAN.R-project.org/package=rvest
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.rvest
- type: software
  title: httr2
  abstract: 'httr2: Perform HTTP Requests and Process the Responses'
  notes: Imports
  url: https://httr2.r-lib.org
  repository: https://CRAN.R-project.org/package=httr2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.httr2
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: BiocGenerics
  abstract: 'BiocGenerics: S4 generic functions used in Bioconductor'
  notes: Suggests
  url: https://bioconductor.org/packages/BiocGenerics
  repository: https://bioconductor.org/
  authors:
  - family-names: Team
    given-names: The Bioconductor Dev
  year: '2024'
  doi: 10.18129/B9.bioc.BiocGenerics
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.testthat
- type: software
  title: covr
  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
  - family-names: Hester
    given-names: Jim
    email: james.f.hester@gmail.com
  year: '2024'
  doi: 10.32614/CRAN.package.covr
- type: software
  title: markdown
  abstract: 'markdown: Render Markdown with ''commonmark'''
  notes: Suggests
  url: https://github.com/rstudio/markdown
  repository: https://CRAN.R-project.org/package=markdown
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Allaire
    given-names: JJ
  - family-names: Horner
    given-names: Jeffrey
  year: '2024'
  doi: 10.32614/CRAN.package.markdown

GitHub Events

Total

Issues event: 7
Watch event: 10
Delete event: 1
Issue comment event: 10
Push event: 15
Create event: 2

Last Year

Issues event: 7
Watch event: 10
Delete event: 1
Issue comment event: 10
Push event: 15
Create event: 2

Committers

Last synced: 8 months ago

All Time

Total Commits: 854
Total Committers: 36
Avg Commits per committer: 23.722
Development Distribution Score (DDS): 0.458

Past Year

Commits: 38
Committers: 1
Avg Commits per committer: 38.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Sean Davis	s**i@g**m	463
sdavis2@mail.nih.gov	s**2@mv@b**8	204
d.tenenbaum	d**m@b**8	32
Dan Tenenbaum	d**a@f**g	26
Nitesh Turaga	n**a@g**m	17
Herve Pages	h**s@f**g	15
hpages@fhcrc.org	h**s@fg@b**8	15
p.aboyoun	p**n@b**8	13
Patrick Aboyoun	u****n	13
J Wokaty	j**y@s**u	8
Alexey Sergushichev	a**x@g**m	6
Vladislav Kamenev	m**r@y**u	4
Bioconductor Git-SVN Bridge	b**c@b**g	3
lshep	l**d@r**g	3
Keith Hughitt	k**t@g**m	3
vobencha	v**n@r**g	2
sethf	s**f@b**8	2
m.carlson	m**n@b**8	2
Seth Falcon	s**n@f**g	2
Hervé Pagès	h**s@f**g	2
Leonardo Gama	l**a@g**m	2
vobencha	v**a@g**m	2
dereckdemezquita	d**k@d**m	2
LiNk-NY	m**9@g**m	1
Giovanni Dall'Olio	d**m@g**m	1
v.obenchain	v**n@b**8	1
c.wong	c**g@b**8	1
Valerie Obenchain	v**a@f**g	1
Marc Carlson	m**n@f**g	1
Chao-Jen Wong	c**2@f**g	1
and 6 more...

Committer Domains (Top 20 + Academic)

fhcrc.org: 7 roswellpark.org: 2 yihui.name: 1 demezquita.com: 1 fredhutch.org: 1 bioconductor.org: 1 ya.ru: 1 sph.cuny.edu: 1 mail.nih.gov: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time

Total issues: 83
Total pull requests: 24
Average time to close issues: about 1 year
Average time to close pull requests: 9 months
Total issue authors: 58
Total pull request authors: 14
Average comments per issue: 2.08
Average comments per pull request: 1.17
Merged pull requests: 17
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 1.67
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

seandavi (16)
khughitt (3)
assaron (3)
DarioS (3)
kalugny (3)
zkyriaki (3)
ghost (2)
aeolianine (1)
1298894527 (1)
davidechicco (1)
Guossin (1)
atakanekiz (1)
dereckmezquita (1)
blancahimes (1)
sionaris (1)

Pull Request Authors

seandavi (5)
assaron (4)
vlakam (2)
dereckmezquita (2)
khughitt (2)
ChemBioScripting (2)
kalugny (1)
grimbough (1)
russHyde (1)
yihui (1)
martinguerrero89 (1)
Yunuuuu (1)
frlender (1)
MichaelChirico (1)

Top Labels

Issue Labels

bug (8) enhancement (6) wontfix (2) question (2) support (2) tests (1) Possible NCBI issue (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 2,138,035 total

Total dependent packages: 47
Total dependent repositories: 0
Total versions: 5
Total maintainers: 1

bioconductor.org: GEOquery

Get data from NCBI Gene Expression Omnibus (GEO)

Homepage: https://github.com/seandavi/GEOquery http://seandavi.github.io/GEOquery http://seandavi.github.io/GEOquery/
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf
License: MIT + file LICENSE
Latest release: 2.76.0
published 9 months ago

Versions: 5
Dependent Packages: 47
Dependent Repositories: 0
Downloads: 2,138,035 Total

Rankings

Dependent repos count: 0.0%

Forks count: 1.3%

Average: 1.4%

Downloads: 1.6%

Dependent packages count: 1.8%

Stargazers count: 2.6%

Maintainers (1)

seandavi@gmail.com

Last synced: 4 months ago

GEOquery

Science Score: 54.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Status

Installation

if needed, install BiocManager

install GEOquery

Usage

How to contribute

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

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Issue Labels

Pull Request Labels

Packages

bioconductor.org: GEOquery

Rankings

Maintainers (1)

Dependencies