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chromatograms

Low level infrastructure to handle chromatograms

https://github.com/rformassspectrometry/chromatograms

Science Score: 44.0%

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Repository

Low level infrastructure to handle chromatograms

Basic Info
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  • Stars: 1
  • Watchers: 3
  • Forks: 1
  • Open Issues: 9
  • Releases: 0
Created about 7 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog Citation

README.md

Low level infrastructure to handle chromatographic data

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov license

This package, part of the R for Mass Spectrometry initiative, provides support for handling and analysing chromatographic mass spectrometry (MS) data.

It follows the API that is currenlty available in the Chromatogram class in the MSnbase package, with support for different backends to provide/represent the data, similar to the Spectra package.

General concept

A Chromatograms object is designed to contain multiple chromatographic data (i.e. chromatogram entities). The data will be stored linearly, i.e. as a long list of chromatograms. The Chromatograms object will be the main object for the end user, providing functionality to access, filter or process chromatographic data, with the actual chromatographic MS data being stored within backend classes. Different implementations of backend classes can be designed for high performance or low memory footprint.

The existing backend classes are:

  • ChromBackendMemory: a memory-based backend, storing the data in memory. This is the default backend and is used for testing purposes.

  • The ChromBackendMzR inherits all slots and methods from the base ChromBackendMemory backend, providing additional functionality for reading chromatographic data from mzML files.

  • ChromBackendSpectra: The ChromBackendSpectra inherits all slots and methods from the base ChromBackendMemory backend, providing additional functionality for reading chromatographic data from Spectra objects.

These backend are then handled on a user level by the Chromatograms class, which provides a unified interface to access and manipulate the chromatographic data.

Installation

install.packages("BiocManager") BiocManager::install("Chromatograms")

Contributions

Please the R for Mass Spectrometry code of conduct and contribution guidelines.

Owner

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

R packages for mass spectrometry

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 "Chromatograms" in publications use:'
type: software
license: Artistic-2.0
title: 'Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data'
version: 0.99.1
abstract: The Chromatograms packages defines a efficient infrastructure for storing
  and handling of chromatographic mass spectrometry data. It provides different implementations
  of *backends* to store and represent the data. Such backends can be optimized for
  small memory footprint or fast data access/processing. A lazy evaluation queue and
  chunk-wise processing capabilities ensure efficient analysis of also very large
  data sets.
authors:
- family-names: Gatto
  given-names: Laurent
  email: laurent.gatto@uclouvain.be
  orcid: https://orcid.org/0000-0002-1520-2268
- family-names: Rainer
  given-names: Johannes
  email: Johannes.Rainer@eurac.edu
  orcid: https://orcid.org/0000-0002-6977-7147
- family-names: Louail
  given-names: Philippine
  email: philippine.louail@outlook.com
  orcid: https://orcid.org/0009-0007-5429-6846
repository: https://bioconductor.org/
repository-code: https://github.com/RforMassSpectrometry/Chromatograms
url: https://github.com/RforMassSpectrometry/Chromatograms
contact:
- family-names: Louail
  given-names: Philippine
  email: philippine.louail@outlook.com
  orcid: https://orcid.org/0009-0007-5429-6846
references:
- type: software
  title: BiocParallel
  abstract: 'BiocParallel: Bioconductor facilities for parallel evaluation'
  notes: Depends
  url: https://github.com/Bioconductor/BiocParallel
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
    email: mtmorgan.bioc@gmail.com
  - family-names: Wang
    given-names: Jiefei
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
  - family-names: Thompson
    given-names: Ryan
    email: rct@thompsonclan.org
  - family-names: Turaga
    given-names: Nitesh
  year: '2025'
  doi: 10.18129/B9.bioc.BiocParallel
- type: software
  title: ProtGenerics
  abstract: 'ProtGenerics: Generic infrastructure for Bioconductor mass spectrometry
    packages'
  notes: Depends
  url: https://github.com/RforMassSpectrometry/ProtGenerics
  repository: https://bioconductor.org/
  authors:
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
  - family-names: Rainer
    given-names: Johannes
    email: johannes.rainer@eurac.edu
  year: '2025'
  doi: 10.18129/B9.bioc.ProtGenerics
  version: '>= 1.39.2'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.5.0'
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- 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: '2025'
  doi: 10.18129/B9.bioc.S4Vectors
- type: software
  title: MsCoreUtils
  abstract: 'MsCoreUtils: Core Utils for Mass Spectrometry Data'
  notes: Imports
  url: https://github.com/RforMassSpectrometry/MsCoreUtils
  repository: https://bioconductor.org/
  authors:
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
    orcid: https://orcid.org/0000-0002-1520-2268
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Gibb
    given-names: Sebastian
    email: mail@sebastiangibb.de
    orcid: https://orcid.org/0000-0001-7406-4443
  - family-names: Louail
    given-names: Philippine
    email: philippine.louail@eurac.edu
    orcid: https://orcid.org/0009-0007-5429-6846
  year: '2025'
  doi: 10.18129/B9.bioc.MsCoreUtils
  version: '>= 1.7.5'
- type: software
  title: msdata
  abstract: 'msdata: Various Mass Spectrometry raw data example files'
  notes: Suggests
  repository: https://bioconductor.org/
  authors:
  - family-names: Neumann
    given-names: Steffen
    email: sneumann@ipb-halle.de
  - family-names: Rainer
    given-names: Laurent Gatto with contriutions from Johannes
    email: laurent.gatto@uclouvain.be
  year: '2025'
  doi: 10.18129/B9.bioc.msdata
  version: '>= 0.19.3'
- type: software
  title: roxygen2
  abstract: 'roxygen2: In-Line Documentation for R'
  notes: Suggests
  url: https://roxygen2.r-lib.org/
  repository: https://CRAN.R-project.org/package=roxygen2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Danenberg
    given-names: Peter
    email: pcd@roxygen.org
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  - family-names: Eugster
    given-names: Manuel
  year: '2025'
  doi: 10.32614/CRAN.package.roxygen2
- type: software
  title: BiocStyle
  abstract: 'BiocStyle: Standard styles for vignettes and other Bioconductor documents'
  notes: Suggests
  url: https://github.com/Bioconductor/BiocStyle
  repository: https://bioconductor.org/
  authors:
  - family-names: Oleś
    given-names: Andrzej
    orcid: https://orcid.org/0000-0003-0285-2787
  year: '2025'
  doi: 10.18129/B9.bioc.BiocStyle
  version: '>= 2.5.19'
- 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: '2025'
  doi: 10.32614/CRAN.package.testthat
- 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: '2025'
  doi: 10.32614/CRAN.package.knitr
  version: '>= 1.1.0'
- 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: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: mzR
  abstract: 'mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry
    data)'
  notes: Suggests
  url: https://github.com/sneumann/mzR/
  repository: https://bioconductor.org/
  authors:
  - family-names: Neumann
    given-names: Steffen
    email: sneumann@ipb-halle.de
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
  - family-names: Kou
    given-names: Qiakng
    email: qkou@umail.iu.edu
  year: '2025'
  doi: 10.18129/B9.bioc.mzR
  version: '>= 2.41.4'
- type: software
  title: Spectra
  abstract: 'Spectra: Spectra Infrastructure for Mass Spectrometry Data'
  notes: Suggests
  url: https://github.com/RforMassSpectrometry/Spectra
  repository: https://bioconductor.org/
  authors:
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
    orcid: https://orcid.org/0000-0002-1520-2268
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Gibb
    given-names: Sebastian
    email: mail@sebastiangibb.de
    orcid: https://orcid.org/0000-0001-7406-4443
  - family-names: Louail
    given-names: Philippine
    email: philippine.louail@eurac.edu
    orcid: https://orcid.org/0009-0007-5429-6846
  year: '2025'
  doi: 10.18129/B9.bioc.Spectra
- type: software
  title: MsBackendMetaboLights
  abstract: 'MsBackendMetaboLights: Retrieve Mass Spectrometry Data from MetaboLights'
  notes: Suggests
  url: https://github.com/RforMassSpectrometry/MsBackendMetaboLights
  repository: https://bioconductor.org/
  authors:
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Louail
    given-names: Philippine
    email: philippine.louail@eurac.edu
    orcid: https://orcid.org/0009-0007-5429-6846
  year: '2025'
  version: '>= 1.3.1'
- type: software
  title: vdiffr
  abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing'
  notes: Suggests
  url: https://vdiffr.r-lib.org/
  repository: https://CRAN.R-project.org/package=vdiffr
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: jake@apache.org
  - family-names: Decorde
    given-names: Matthieu
    email: matthieu.decorde@ens-lyon.fr
  - family-names: Lise
    given-names: Vaudor
    email: lise.vaudor@ens-lyon.fr
  year: '2025'
  doi: 10.32614/CRAN.package.vdiffr

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Last Year
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Last synced: 10 months ago

All Time
  • Total issues: 12
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  • Average time to close issues: 6 months
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Past Year
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Dependencies

DESCRIPTION cran
  • ProtGenerics >= 1.17.4 depends
  • BiocGenerics * imports
  • BiocParallel * imports
  • IRanges * imports
  • MsCoreUtils >= 0.0.2 imports
  • S4Vectors * imports
  • methods * imports
  • knitr >= 1.1.0 suggests
  • msdata >= 0.19.3 suggests
  • mzR >= 2.15.1 suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite