vignettes/MyBioconductorPackage.Rmd
MyBioconductorPackage.RmdMyBioconductorPackage
R is an open-source statistical environment which can be
easily modified to enhance its functionality via packages. MyBioconductorPackage
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
MyBioconductorPackage
by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("MyBioconductorPackage")
## Check that you have a valid Bioconductor installation
BiocManager::valid()MyBioconductorPackage is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with RNA-seq data (EDIT!). That is, packages like SummarizedExperiment (EDIT!).
If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.
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
MyBioconductorPackage 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.
MyBioconductorPackage
We hope that MyBioconductorPackage will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("MyBioconductorPackage")
#>
#> To cite package 'MyBioconductorPackage' in publications use:
#>
#> kevinrue (2022). _Demonstration of a Bioconductor Package_.
#> doi:10.18129/B9.bioc.MyBioconductorPackage
#> <https://doi.org/10.18129/B9.bioc.MyBioconductorPackage>,
#> https://github.com/kevinrue/MyBioconductorPackage/MyBioconductorPackage
#> - R package version 0.99.0,
#> <http://www.bioconductor.org/packages/MyBioconductorPackage>.
#>
#> kevinrue (2022). "Demonstration of a Bioconductor Package."
#> _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
#> <https://www.biorxiv.org/content/10.1101/TODO>.
#>
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.MyBioconductorPackage
Edit this as you see fit =)
Here is an example of you can cite your package inside the vignette:
The MyBioconductorPackage package (kevinrue, 2022) was made possible thanks to:
This package was developed using biocthis.
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("MyBioconductorPackage.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("MyBioconductorPackage.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2022-10-21 15:33:58 UTC"Wallclock time spent generating the vignette.
#> Time difference of 0.923 secsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2022-10-21
#> pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] RSPM (R 4.2.0)
#> bibtex 0.5.0 2022-09-25 [1] RSPM (R 4.2.0)
#> BiocManager 1.30.18 2022-05-18 [2] CRAN (R 4.2.1)
#> BiocStyle * 2.25.0 2022-04-26 [1] Bioconductor
#> bookdown 0.29 2022-09-12 [1] RSPM (R 4.2.0)
#> bslib 0.4.0 2022-07-16 [2] RSPM (R 4.2.0)
#> cachem 1.0.6 2021-08-19 [2] RSPM (R 4.2.0)
#> cli 3.4.1 2022-09-23 [2] RSPM (R 4.2.0)
#> desc 1.4.2 2022-09-08 [2] RSPM (R 4.2.0)
#> digest 0.6.30 2022-10-18 [2] RSPM (R 4.2.0)
#> evaluate 0.17 2022-10-07 [2] RSPM (R 4.2.0)
#> fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.2.0)
#> fs 1.5.2 2021-12-08 [2] RSPM (R 4.2.0)
#> generics 0.1.3 2022-07-05 [1] RSPM (R 4.2.0)
#> htmltools 0.5.3 2022-07-18 [2] RSPM (R 4.2.0)
#> httr 1.4.4 2022-08-17 [2] RSPM (R 4.2.0)
#> jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.2.0)
#> jsonlite 1.8.2 2022-10-02 [2] RSPM (R 4.2.0)
#> knitr 1.40 2022-08-24 [2] RSPM (R 4.2.0)
#> lubridate 1.8.0 2021-10-07 [1] RSPM (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.2.0)
#> memoise 2.0.1 2021-11-26 [2] RSPM (R 4.2.0)
#> MyBioconductorPackage * 0.99.0 2022-10-21 [1] Bioconductor
#> pkgdown 2.0.6 2022-07-16 [2] RSPM (R 4.2.0)
#> plyr 1.8.7 2022-03-24 [1] RSPM (R 4.2.0)
#> purrr 0.3.5 2022-10-06 [2] RSPM (R 4.2.0)
#> R6 2.5.1 2021-08-19 [2] RSPM (R 4.2.0)
#> ragg 1.2.3 2022-09-29 [2] RSPM (R 4.2.0)
#> Rcpp 1.0.9 2022-07-08 [2] RSPM (R 4.2.0)
#> RefManageR * 1.4.0 2022-09-30 [1] RSPM (R 4.2.0)
#> rlang 1.0.6 2022-09-24 [2] RSPM (R 4.2.0)
#> rmarkdown 2.17 2022-10-07 [2] RSPM (R 4.2.0)
#> rprojroot 2.0.3 2022-04-02 [2] RSPM (R 4.2.0)
#> sass 0.4.2 2022-07-16 [2] RSPM (R 4.2.0)
#> sessioninfo * 1.2.2 2021-12-06 [2] RSPM (R 4.2.0)
#> stringi 1.7.8 2022-07-11 [2] RSPM (R 4.2.0)
#> stringr 1.4.1 2022-08-20 [2] RSPM (R 4.2.0)
#> systemfonts 1.0.4 2022-02-11 [2] RSPM (R 4.2.0)
#> textshaping 0.3.6 2021-10-13 [2] RSPM (R 4.2.0)
#> xfun 0.34 2022-10-18 [2] RSPM (R 4.2.0)
#> xml2 1.3.3 2021-11-30 [2] RSPM (R 4.2.0)
#> yaml 2.3.6 2022-10-18 [2] RSPM (R 4.2.0)
#>
#> [1] /__w/_temp/Library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/local/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────This vignette was generated using BiocStyle (Oleś, 2022) with knitr (Xie, 2022) and rmarkdown (Allaire, Xie, McPherson et al., 2022) running behind the scenes.
Citations made with RefManageR (McLean, 2017).
[1] J. Allaire, Y. Xie, J. McPherson, et al. rmarkdown: Dynamic Documents for R. R package version 2.17. 2022. URL: https://github.com/rstudio/rmarkdown.
[2] kevinrue. Demonstration of a Bioconductor Package. https://github.com/kevinrue/MyBioconductorPackage/MyBioconductorPackage - R package version 0.99.0. 2022. DOI: 10.18129/B9.bioc.MyBioconductorPackage. URL: http://www.bioconductor.org/packages/MyBioconductorPackage.
[3] 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.
[4] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.25.0. 2022. URL: https://github.com/Bioconductor/BiocStyle.
[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2022. 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. https://github.com/r-lib/sessioninfo#readme, https://r-lib.github.io/sessioninfo/. 2021.
[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.40. 2022. URL: https://yihui.org/knitr/.