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MsBackendSql

MsBackend adding support to store/access mass spectrometry data in large SQL databases through the Spectra R package.

https://github.com/rformassspectrometry/msbackendsql

Science Score: 26.0%

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary

Keywords from Contributors

bioconductor-package
Last synced: 10 months ago · JSON representation

Repository

MsBackend adding support to store/access mass spectrometry data in large SQL databases through the Spectra R package.

Basic Info
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 0
  • Open Issues: 3
  • Releases: 0
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog

README.md

SQL-based Mass Spectrometry Data Backend

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov license years in bioc Ranking by downloads build release build devel

This repository provides a backend for Spectra objects that supports storage of mass spectrometry (MS) data in an SQL database. The package provides the functionality to create such databases from original (raw) MS data files (in mzML, mzXML or netCDF format) and allows to extract the data in an efficient way.

For more information see the package homepage.

Creating a database

By providing the connection to an SQL database, the createMsBackendSqlDatabase imports raw MS data from provided file names and stores it into the dedicated database tables created during import. While MsBackendSql supports any type of SQL database, it is currently optimized for MySQL/MariaDB databases.

Using a MsBackendSql database

MS data in a MsBackendSql database can be accessed through the Spectra package by using the MsBackendSql MS backend. Assuming the variable dbcon represents a (RDBI) database connection to a MsBackendSql, the data can be represented/used with a Spectra object by:

r library(Spectra) library(MsBackendSql) sps <- Spectra(dbcon, source = MsBackendSql())

For more information see the package homepage.

Installation

The package can be installed with

r install.packages("BiocManager") BiocManager::install("MsBackendSql")

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.

Owner

  • Name: RforMassSpectrometry
  • Login: rformassspectrometry
  • Kind: organization
  • Email: maintainer@rformassspectrometry.org

R packages for mass spectrometry

GitHub Events

Total
  • Issue comment event: 1
  • Push event: 23
  • Pull request review event: 5
  • Pull request review comment event: 6
  • Pull request event: 9
Last Year
  • Issue comment event: 1
  • Push event: 23
  • Pull request review event: 5
  • Pull request review comment event: 6
  • Pull request event: 9

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 69
  • Total Committers: 2
  • Avg Commits per committer: 34.5
  • Development Distribution Score (DDS): 0.029
Past Year
  • Commits: 36
  • Committers: 2
  • Avg Commits per committer: 18.0
  • Development Distribution Score (DDS): 0.056
Top Committers
Name Email Commits
jorainer j****r@g****m 67
J Wokaty j****y 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 6
  • Total pull requests: 23
  • Average time to close issues: 4 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 2.5
  • Average comments per pull request: 0.22
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.22
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jorainer (5)
Pull Request Authors
  • jorainer (25)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 5,458 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: MsBackendSql

SQL-based Mass Spectrometry Data Backend

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,458 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 19.8%
Stargazers count: 21.8%
Average: 27.9%
Downloads: 98.1%
Maintainers (1)
Johannes.Rainer@eurac.edu
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • Spectra >= 1.5.17 depends
  • BiocParallel * imports
  • DBI * imports
  • IRanges * imports
  • MsCoreUtils * imports
  • ProtGenerics * imports
  • S4Vectors * imports
  • data.table * imports
  • methods * imports
  • progress * imports
  • BiocStyle >= 2.5.19 suggests
  • RSQLite * suggests
  • knitr >= 1.1.0 suggests
  • msdata * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite