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TargetSearch

R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.

https://github.com/acinostroza/targetsearch

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 14 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary

Keywords

bioc bioconductor gc-ms mass-spectrometry

Keywords from Contributors

bioconductor-package bioinformatics pathway-analysis mirror image-analysis rhdf5 hdf5 rnaseq derfinder reproducibility
Last synced: 6 months ago · JSON representation

Repository

R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.

Basic Info
  • Host: GitHub
  • Owner: acinostroza
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 1.06 MB
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
bioc bioconductor gc-ms mass-spectrometry
Created almost 8 years ago · Last pushed 7 months ago
Metadata Files
Readme

README.md

TargetSearch

platforms rank in Bioc build updated dependencies

This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.

This software is part of the Bioconductor project.

https://bioconductor.org/packages/release/bioc/html/TargetSearch.html

This git repository mirrors the TargetSearch git repository on Bioconductor, which is available here: https://code.bioconductor.org/browse/TargetSearch/

Installation

Please follow the instructions on TargetSearch's page on Bioconductor site linked above. In short:

``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("TargetSearch") ```

Citation

Cuadros-Inostroza A, Caldana C, Redestig H, Lisec J, Pena-Cortes H, Willmitzer L, Hannah MA (2009). "TargetSearch - a Bioconductor package for the efficient pre-processing of GC-MS metabolite profiling data." BMC Bioinformatics, 10, 428. doi:10.1186/1471-2105-10-428.

Bugs

Please report bugs at https://github.com/acinostroza/TargetSearch/issues

License

The code is licensed under the GNU Public License version 2.0 or greater (SPDX License ID: GPL-2.0-or-later).

To obtain a copy of the license, see: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html

Owner

  • Name: Alvaro Cuadros-Inostroza
  • Login: acinostroza
  • Kind: user

GitHub Events

Total
  • Push event: 8
  • Create event: 3
Last Year
  • Push event: 8
  • Create event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 425
  • Total Committers: 14
  • Avg Commits per committer: 30.357
  • Development Distribution Score (DDS): 0.313
Past Year
  • Commits: 59
  • Committers: 3
  • Avg Commits per committer: 19.667
  • Development Distribution Score (DDS): 0.102
Top Committers
Name Email Commits
Alvaro Cuadros-Inostroza a****b@g****m 292
Alvaro Cuadros-Inostroza i****a@m****e 63
Dan Tenenbaum d****a@f****g 25
Nitesh Turaga n****a@g****m 14
Patrick Aboyoun u****n 8
Herve Pages h****s@f****g 7
J Wokaty j****y@s****u 4
Hervé Pagès h****s@f****g 3
vobencha v****n@r****g 2
J Wokaty j****y 2
vobencha v****a@g****m 2
Sonali Arora s****a@f****g 1
Nishant Gopalakrishnan n****k@f****g 1
Valerie Obenchain v****a@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 5 roswellpark.org: 1 fredhutch.org: 1 sph.cuny.edu: 1 mpimp-golm.mpg.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: 3 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • QizhiSu (1)
Pull Request Authors
  • acinostroza (1)
Top Labels
Issue Labels
question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 36,794 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
  • Total maintainers: 1
bioconductor.org: TargetSearch

A package for the analysis of GC-MS metabolite profiling data

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 36,794 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 12.3%
Stargazers count: 19.5%
Forks count: 19.8%
Downloads: 22.2%
Maintainers (1)
acuadros+bioc@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • assertthat * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • ncdf4 * imports
  • stats * imports
  • utils * imports
  • BiocStyle * suggests
  • TargetSearchData * suggests
  • knitr * suggests
  • tinytest * suggests