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subMALDI

subMALDI: an open framework R package for processing irregularly-spaced mass spectrometry data - Published in JOSS (2021)

https://github.com/wesleyburr/submaldi

Science Score: 93.0%

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    Found 4 DOI reference(s) in README and JOSS metadata
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    Links to: joss.theoj.org
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Last synced: 6 months ago · JSON representation

Repository

subMaldi: a package for R

Basic Info
  • Host: GitHub
  • Owner: wesleyburr
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 126 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 3
  • Open Issues: 0
  • Releases: 7
Created over 6 years ago · Last pushed over 4 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

subMaldi

DOI

subMALDI is an open framework package for the R programming environment that permits organization, pre-processing (smoothing, baseline correction, peak detection), and normalization of spectral data sets. As a result of the package's design, subMALDI data objects are compatible with functions from a wide variety of other R packages, and user-defined functions are easier to implement and test.

Installing in R

To install this package in R, begin by downloading the source copy of the package from the releases folder and install it using type = "source". But, before you do this, a dependency from the BioConductor project is required. Begin by installing the BioConductor Manager:

install.packages("BiocManager")

and then install the package MassSpecWavelet:

BiocManager::install("MassSpecWavelet")

Then install the CRAN-supported packages required:

install.packages(c("tidyr", "ggplot2", "ggpmisc", "reshape2", "RColorBrewer", "signal"))

Once the packages are all installed, you can then install the package:

install.packages("subMALDI-1.0-2.tar.gz", type = "source")

Update the file name as necessary to whatever the copy you downloaded was set to for versioning.

Note: if you install from source, and set dependencies = TRUE, this should all be moot. This assumes you run the commands exactly as given, in which case, the BioConductor sequence doesn't always seem to work. For example,

install.packages("subMALDI-1.0-2.tar.gz", type = "source", dependencies = TRUE)

Getting Started

Refer to the vignette on workflow for a brief summary of the package functionality, and the vignette on processing for a simple example.

Contributing?

Examine our contribution guidelines for more.

Owner

  • Name: Wesley Burr
  • Login: wesleyburr
  • Kind: user
  • Location: Peterborough, Ontario
  • Company: Trent University

Associate Professor of Statistics, Department of Mathematics, Trent University.

JOSS Publication

subMALDI: an open framework R package for processing irregularly-spaced mass spectrometry data
Published
September 10, 2021
DOI
Volume 6, Issue 65, Page 2694
Authors
Kristen Yeh ORCID
Forensic Science Program, Trent University
Sophie Castel ORCID
Faculty of Science, Mathematics, Trent University
Naomi L. Stock ORCID
Water Quality Center, Trent University
Theresa Stotesbury ORCID
Faculty of Science, Forensic Science & Applied Bioscience, Ontario Tech University
Wesley Burr ORCID
Faculty of Science, Mathematics, Trent University
Editor
Amy Roberts ORCID
Tags
mass spectrometry spectral processing MALDI-MS
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GitHub Events

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Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 689
  • Total Committers: 3
  • Avg Commits per committer: 229.667
  • Development Distribution Score (DDS): 0.601
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Kristen Yeh k****h@t****a 275
Sophie Castel s****l@t****a 260
Wesley Burr w****r@g****m 154
Committer Domains (Top 20 + Academic)
trentu.ca: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 22
  • Total pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: less than a minute
  • Total issue authors: 5
  • Total pull request authors: 1
  • Average comments per issue: 1.23
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • 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
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Top Authors
Issue Authors
  • wesleyburr (16)
  • kristenyeh (3)
  • sigven (1)
  • tystan (1)
  • jspaezp (1)
Pull Request Authors
  • wesleyburr (1)
Top Labels
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help wanted (4)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • MassSpecWavelet >= 1.48.0 imports
  • RColorBrewer >= 1.1 imports
  • dplyr >= 0.8.0 imports
  • ggplot2 >= 3.3.0 imports
  • ggpmisc >= 0.3.3 imports
  • reshape2 >= 1.4.4 imports
  • signal >= 0.7 imports
  • tidyr >= 1.1.0 imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests