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spang-lab / metabodecon

Deconvolution of 1D NMR spectra using MetaboDecon1D followed by alignment of the data by the speaq package and some additional postprocessing resulting in an aligned data matrix of aligned signal integrals
https://spang-lab.github.io/metabodecon/
GNU General Public License v3.0
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readme

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metabodecon man/figures/logo.svg

A package for deconvolution of 1D NMR spectra using MetaboDecon1D followed by alignment of the data using the speaq package and some additional post-processing, resulting in a data matrix of aligned signal integrals.

Installation

Copy paste the following command in a running R session (e.g. in RStudio):

if (!"devtools" %in% installed.packages()[, "Package"]) {
    install.packages("devtools", repos = c(CRAN = "https://cloud.r-project.org"))
}
devtools::install_github("spang-lab/metabodecon", build_manual = TRUE, build_vignettes = TRUE)

Usage

At Get Started you can see an example how metabodecon can be used to deconvolute an existing data set, followed by alignment of the data and some additional postprocessing steps, resulting in a data matrix of aligned signal integrals.

At Function Reference you get an overview of all function provided by metabodecon.

Contribute

Things you can update, are:

  1. Function code in folder R
  2. Function documentation in folder R
  3. Package documentation in folder vignettes
  4. Test cases in folder tests
  5. Dependencies in file DESCRIPTION
  6. Authors in file DESCRIPTION

Whenever you update any of those things, you should run the below commands to check that everything is still working as expected

devtools::test() # Execute tests from tests folder
devtools::document() # Build files in man folder
devtools::check() # Check package formalities
devtools::install() # Install as required by next command
pkgdown::build_site() # Build website in docs folder

After doing these steps, you can push your changes to Github and then use the following commands to release the package to CRAN:

devtools::check(remote = TRUE, manual = TRUE)# Slower, but more realistic test than plain devtools::check()
devtools::spell_check() # Check spelling. Add false positives to inst/WORDLIST
revdepcheck::revdep_check(num_workers = 8) # Reverse dependency check
# See https://r-pkgs.org/release.html#sec-release-revdep-checks for details
devtools::submit_cran() # Submits the package to CRAN

Above steps are based on: https://r-pkgs.org/release.html