1-Package introduction

Basics

Install `PhenolicsDB`

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. PhenolicsDB is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install PhenolicsDB by using the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
  }

BiocManager::install("PhenolicsDB")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

Required knowledge

PhenolicsDB is a data package that contains MS/MS data of authentic analytical standads. Therefore, in order to be familiar with what data you will find in this package, you will need to be familiar with mass spectrometry.

If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.

Asking for help

As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But R and Bioconductor have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the PhenolicsDB tag and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.

Citing `PhenolicsDB`

We hope that PhenolicsDB will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("PhenolicsDB")
#> To cite PhenolicsDB in publications use:
#> 
#>   Quiroz-Moreno C, Cooperstone J (2023). _PhenolicsDB: phenolics MS/MS
#>   (LC-ESI-QTOF) database repository_. doi:10.5281/zenodo.8475
#>   <https://doi.org/10.5281/zenodo.8475>,
#>   <https://cooperstonelab.github.io/PhenolicsDB/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {PhenolicsDB: phenolics MS/MS (LC-ESI-QTOF) database repository},
#>     author = {Cristian Quiroz-Moreno and Jessica Cooperstone},
#>     year = {2023},
#>     doi = {10.5281/zenodo.8475},
#>     url = {https://cooperstonelab.github.io/PhenolicsDB/},
#>   }

Reproducibility

The PhenolicsDB package (Quiroz-Moreno and Cooperstone, 2023) was made possible thanks to:

R (R Core Team, 2024)
BiocStyle (Oleś, 2024)
knitr (Xie, 2024)
RefManageR (McLean, 2017)
rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2024)
sessioninfo (Wickham, Chang, Flight, Müller, and Hester, 2021)
testthat (Wickham, 2011)

This package was developed using biocthis.

Code for creating the vignette

## Create the vignette
library("rmarkdown")
system.time(render("PhenolicsDB_intro.Rmd", "BiocStyle::html_document"))

## Extract the R code
library("knitr")
knit("PhenolicsDB_intro.Rmd", tangle = TRUE)

Date the vignette was generated.

#> [1] "2024-10-23 18:06:57 UTC"

Wallclock time spent generating the vignette.

#> Time difference of 0.969 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.1 (2024-06-14)
#>  os       Ubuntu 22.04.5 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en
#>  collate  C.UTF-8
#>  ctype    C.UTF-8
#>  tz       UTC
#>  date     2024-10-23
#>  pandoc   3.1.11 @ /opt/hostedtoolcache/pandoc/3.1.11/x64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  backports     1.5.0   2024-05-23 [1] RSPM
#>  bibtex        0.5.1   2023-01-26 [1] RSPM
#>  BiocManager   1.30.25 2024-08-28 [1] RSPM
#>  BiocStyle   * 2.32.1  2024-06-16 [1] Bioconduc~
#>  bookdown      0.41    2024-10-16 [1] RSPM
#>  bslib         0.8.0   2024-07-29 [1] RSPM
#>  cachem        1.1.0   2024-05-16 [1] RSPM
#>  cli           3.6.3   2024-06-21 [1] RSPM
#>  desc          1.4.3   2023-12-10 [1] RSPM
#>  digest        0.6.37  2024-08-19 [1] RSPM
#>  evaluate      1.0.1   2024-10-10 [1] RSPM
#>  fastmap       1.2.0   2024-05-15 [1] RSPM
#>  fs            1.6.4   2024-04-25 [1] RSPM
#>  generics      0.1.3   2022-07-05 [1] RSPM
#>  glue          1.8.0   2024-09-30 [1] RSPM
#>  htmltools     0.5.8.1 2024-04-04 [1] RSPM
#>  httr          1.4.7   2023-08-15 [1] RSPM
#>  jquerylib     0.1.4   2021-04-26 [1] RSPM
#>  jsonlite      1.8.9   2024-09-20 [1] RSPM
#>  knitr         1.48    2024-07-07 [1] RSPM
#>  lifecycle     1.0.4   2023-11-07 [1] RSPM
#>  lubridate     1.9.3   2023-09-27 [1] RSPM
#>  magrittr      2.0.3   2022-03-30 [1] RSPM
#>  pkgdown       2.1.1   2024-09-17 [1] any (@2.1.1)
#>  plyr          1.8.9   2023-10-02 [1] RSPM
#>  R6            2.5.1   2021-08-19 [1] RSPM
#>  ragg          1.3.3   2024-09-11 [1] RSPM
#>  Rcpp          1.0.13  2024-07-17 [1] RSPM
#>  RefManageR  * 1.4.0   2022-09-30 [1] RSPM
#>  rlang         1.1.4   2024-06-04 [1] RSPM
#>  rmarkdown     2.28    2024-08-17 [1] RSPM
#>  sass          0.4.9   2024-03-15 [1] RSPM
#>  sessioninfo * 1.2.2   2021-12-06 [1] RSPM
#>  stringi       1.8.4   2024-05-06 [1] RSPM
#>  stringr       1.5.1   2023-11-14 [1] RSPM
#>  systemfonts   1.1.0   2024-05-15 [1] RSPM
#>  textshaping   0.4.0   2024-05-24 [1] RSPM
#>  timechange    0.3.0   2024-01-18 [1] RSPM
#>  xfun          0.48    2024-10-03 [1] RSPM
#>  xml2          1.3.6   2023-12-04 [1] RSPM
#>  yaml          2.3.10  2024-07-26 [1] RSPM
#> 
#>  [1] /home/runner/work/_temp/Library
#>  [2] /opt/R/4.4.1/lib/R/site-library
#>  [3] /opt/R/4.4.1/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Bibliography

This vignette was generated using BiocStyle (Oleś, 2024) with knitr (Xie, 2024) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.28. 2024. URL: https://github.com/rstudio/rmarkdown.

[2] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.

[3] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.32.1. 2024. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.

[4] C. Quiroz-Moreno and J. Cooperstone. PhenolicsDB: phenolics MS/MS (LC-ESI-QTOF) database repository. 2023. DOI: 10.5281/zenodo.8475. URL: https://cooperstonelab.github.io/PhenolicsDB/.

[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2024. URL: https://www.R-project.org/.

[6] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.

[7] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.2, https://r-lib.github.io/sessioninfo/. 2021. URL: https://github.com/r-lib/sessioninfo#readme.

[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.48. 2024. URL: https://yihui.org/knitr/.

Daniel Quiroz and Jessica Cooperstone

23 October 2024

Basics

Install `PhenolicsDB`

Required knowledge

Asking for help

Citing `PhenolicsDB`

Reproducibility

Bibliography

1-Package introduction

Daniel Quiroz and Jessica Cooperstone

23 October 2024

Basics

Install PhenolicsDB

Required knowledge

Asking for help

Citing PhenolicsDB

Reproducibility

Bibliography

Install `PhenolicsDB`

Citing `PhenolicsDB`