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masssight

An R package for the alignment and scaling of LC-MS metabolomics data

https://github.com/omicseye/masssight

Science Score: 44.0%

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Keywords

batch-correction metabolomics omics r
Last synced: 6 months ago · JSON representation ·

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An R package for the alignment and scaling of LC-MS metabolomics data

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  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 3
Topics
batch-correction metabolomics omics r
Created almost 3 years ago · Last pushed 8 months ago
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Owner

  • Name: omicsEye
  • Login: omicsEye
  • Kind: organization
  • Location: Rahnavard Lab at Computational Biology Institute, George Washington University

Understanding biology via novel machine learning, statistical, and visualization techniques on omics data for public health and precision medicine

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 "massSight" in publications use:'
type: software
license: MIT
title: 'massSight: Batch Alignment and Scaling for LC-MS Data'
version: 0.2.2
abstract: an `R` package for the alignment, scaling, and downstream analysis of LC-MS
  metabolomics data.
authors:
- family-names: Gohel
  given-names: Chiraag
  email: chiraaggohel@gwu.edu
  orcid: https://orcid.org/0000-0003-4446-9380
- family-names: Sayoldin
  given-names: Bahar
  email: sayoldin@gwu.edu
  orcid: https://orcid.org/0000-0003-1187-0848
- family-names: Rahnavard
  given-names: Ali
  email: rahnavard@gwu.edu
  orcid: https://orcid.org/0000-0002-9710-0248
repository: https://bioconductor.org/
repository-code: https://github.com/omicsEye/massSight
url: https://omicseye.github.io/massSight/
contact:
- family-names: Gohel
  given-names: Chiraag
  email: chiraaggohel@gwu.edu
  orcid: https://orcid.org/0000-0003-4446-9380
keywords:
- batch-correction
- metabolomics
- omics
- r
references:
- 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: '2024'
  version: '>= 3.5'
- type: software
  title: caret
  abstract: 'caret: Classification and Regression Training'
  notes: Imports
  url: https://github.com/topepo/caret/
  repository: https://CRAN.R-project.org/package=caret
  authors:
  - family-names: Kuhn
    given-names: Max
    email: mxkuhn@gmail.com
    orcid: https://orcid.org/0000-0003-2402-136X
  year: '2024'
  doi: 10.32614/CRAN.package.caret
- type: software
  title: checkmate
  abstract: 'checkmate: Fast and Versatile Argument Checks'
  notes: Imports
  url: https://mllg.github.io/checkmate/
  repository: https://CRAN.R-project.org/package=checkmate
  authors:
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
    orcid: https://orcid.org/0000-0001-9754-0393
  year: '2024'
  doi: 10.32614/CRAN.package.checkmate
- type: software
  title: cowplot
  abstract: 'cowplot: Streamlined Plot Theme and Plot Annotations for ''ggplot2'''
  notes: Imports
  url: https://wilkelab.org/cowplot/
  repository: https://CRAN.R-project.org/package=cowplot
  authors:
  - family-names: Wilke
    given-names: Claus O.
    email: wilke@austin.utexas.edu
    orcid: https://orcid.org/0000-0002-7470-9261
  year: '2024'
  doi: 10.32614/CRAN.package.cowplot
- 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: dbscan
  abstract: 'dbscan: Density-Based Spatial Clustering of Applications with Noise (DBSCAN)
    and Related Algorithms'
  notes: Imports
  url: https://github.com/mhahsler/dbscan
  repository: https://CRAN.R-project.org/package=dbscan
  authors:
  - family-names: Hahsler
    given-names: Michael
    email: mhahsler@lyle.smu.edu
    orcid: https://orcid.org/0000-0003-2716-1405
  - family-names: Piekenbrock
    given-names: Matthew
  year: '2024'
  doi: 10.32614/CRAN.package.dbscan
- 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: GauPro
  abstract: 'GauPro: Gaussian Process Fitting'
  notes: Imports
  url: https://github.com/CollinErickson/GauPro
  repository: https://CRAN.R-project.org/package=GauPro
  authors:
  - family-names: Erickson
    given-names: Collin
  year: '2024'
  doi: 10.32614/CRAN.package.GauPro
- type: software
  title: ggExtra
  abstract: 'ggExtra: Add Marginal Histograms to ''ggplot2'', and More ''ggplot2''
    Enhancements'
  notes: Imports
  url: https://daattali.com/shiny/ggExtra-ggMarginal-demo/
  repository: https://CRAN.R-project.org/package=ggExtra
  authors:
  - family-names: Attali
    given-names: Dean
    email: daattali@gmail.com
  - family-names: Baker
    given-names: Christopher
    email: chriscrewbaker@gmail.com
  year: '2024'
  doi: 10.32614/CRAN.package.ggExtra
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2024'
  doi: 10.32614/CRAN.package.ggplot2
- type: software
  title: logr
  abstract: 'logr: Creates Log Files'
  notes: Imports
  url: https://logr.r-sassy.org
  repository: https://CRAN.R-project.org/package=logr
  authors:
  - family-names: Bosak
    given-names: David
    email: dbosak01@gmail.com
  year: '2024'
  doi: 10.32614/CRAN.package.logr
- 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: 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: '2024'
  doi: 10.32614/CRAN.package.methods
- type: software
  title: mgcv
  abstract: 'mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation'
  notes: Imports
  repository: https://CRAN.R-project.org/package=mgcv
  authors:
  - family-names: Wood
    given-names: Simon
    email: simon.wood@r-project.org
  year: '2024'
  doi: 10.32614/CRAN.package.mgcv
- type: software
  title: progress
  abstract: 'progress: Terminal Progress Bars'
  notes: Imports
  url: https://github.com/r-lib/progress#readme
  repository: https://CRAN.R-project.org/package=progress
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  - family-names: FitzJohn
    given-names: Rich
  year: '2024'
  doi: 10.32614/CRAN.package.progress
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  year: '2024'
  doi: 10.32614/CRAN.package.purrr
- type: software
  title: Rcpp
  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: Imports
  url: https://www.rcpp.org
  repository: https://CRAN.R-project.org/package=Rcpp
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
  - family-names: Francois
    given-names: Romain
  - family-names: Allaire
    given-names: JJ
  - family-names: Ushey
    given-names: Kevin
  - family-names: Kou
    given-names: Qiang
  - family-names: Russell
    given-names: Nathan
  - family-names: Ucar
    given-names: Inaki
  - family-names: Bates
    given-names: Douglas
  - family-names: Chambers
    given-names: John
  year: '2024'
  doi: 10.32614/CRAN.package.Rcpp
- type: software
  title: readxl
  abstract: 'readxl: Read Excel Files'
  notes: Imports
  url: https://readxl.tidyverse.org
  repository: https://CRAN.R-project.org/package=readxl
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - 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.readxl
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: stats
  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: '2024'
  doi: 10.32614/CRAN.package.stats
- 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: 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: utils
  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: '2024'
  doi: 10.32614/CRAN.package.utils
- type: software
  title: jsonlite
  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
  notes: Suggests
  url: https://jeroen.r-universe.dev/jsonlite
  repository: https://CRAN.R-project.org/package=jsonlite
  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.jsonlite
- 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: 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
  version: '>= 3.0.0'
- type: software
  title: usethis
  abstract: 'usethis: Automate Package and Project Setup'
  notes: Suggests
  url: https://usethis.r-lib.org
  repository: https://CRAN.R-project.org/package=usethis
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  - family-names: Barrett
    given-names: Malcolm
    email: malcolmbarrett@gmail.com
    orcid: https://orcid.org/0000-0003-0299-5825
  - family-names: Teucher
    given-names: Andy
    email: andy.teucher@posit.co
    orcid: https://orcid.org/0000-0002-7840-692X
  year: '2024'
  doi: 10.32614/CRAN.package.usethis

GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Public event: 1
  • Push event: 40
  • Gollum event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Public event: 1
  • Push event: 40
  • Gollum event: 1

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • GauPro * imports
  • dplyr * imports
  • openxlsx * imports
  • patchwork * imports
  • pracma * imports
  • purrr * imports
  • readxl * imports
  • stats * imports
  • stringr * imports
  • xlsx * imports
  • knitr * suggests
  • rmarkdown * suggests