Introduction to iSEEGenerics

Basics

Install `iSEEGenerics`

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. iSEEGenerics 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 iSEEGenerics by using the following commands in your R session:

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

BiocManager::install("iSEEGenerics")

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

Required knowledge

iSEEGenerics 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.

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 iSEEGenerics 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 `iSEEGenerics`

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

## Citation info
citation("iSEEGenerics")
#> 
#> To cite package 'iSEEGenerics' in publications use:
#> 
#>   iSEE (2022). _Demonstration of a Bioconductor Package_.
#>   doi:10.18129/B9.bioc.iSEEGenerics
#>   <https://doi.org/10.18129/B9.bioc.iSEEGenerics>,
#>   https://github.com/iSEE/iSEEGenerics/iSEEGenerics - R package version
#>   0.99.0, <http://www.bioconductor.org/packages/iSEEGenerics>.
#> 
#>   iSEE (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)'.

Quick start to using to `iSEEGenerics`

library("iSEEGenerics")

Edit this as you see fit =)

Here is an example of you can cite your package inside the vignette:

iSEEGenerics (iSEE, 2022)

Reproducibility

The iSEEGenerics package (iSEE, 2022) was made possible thanks to:

R (R Core Team, 2022)
BiocStyle (Oleś, 2022)
knitr (Xie, 2022)
RefManageR (McLean, 2017)
rmarkdown (Allaire, Xie, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2022)
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("iSEEGenerics.Rmd", "BiocStyle::html_document"))

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

Date the vignette was generated.

#> [1] "2022-10-09 14:23:53 UTC"

Wallclock time spent generating the vignette.

#> Time difference of 6.734 secs

R 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     2022-10-09
#>  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)
#>  Biobase              * 2.57.1     2022-05-19 [1] Bioconductor
#>  BiocGenerics         * 0.43.4     2022-09-11 [1] Bioconductor
#>  BiocManager            1.30.18    2022-05-18 [2] CRAN (R 4.2.1)
#>  BiocStyle            * 2.25.0     2022-04-26 [1] Bioconductor
#>  bitops                 1.0-7      2021-04-24 [1] RSPM (R 4.2.0)
#>  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)
#>  DelayedArray           0.23.2     2022-09-14 [1] Bioconductor
#>  desc                   1.4.2      2022-09-08 [2] RSPM (R 4.2.0)
#>  digest                 0.6.29     2021-12-01 [2] RSPM (R 4.2.0)
#>  evaluate               0.16       2022-08-09 [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)
#>  GenomeInfoDb         * 1.33.7     2022-09-07 [1] Bioconductor
#>  GenomeInfoDbData       1.2.9      2022-10-04 [1] Bioconductor
#>  GenomicRanges        * 1.49.1     2022-08-18 [1] Bioconductor
#>  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)
#>  IRanges              * 2.31.2     2022-08-18 [1] Bioconductor
#>  iSEEGenerics         * 0.99.0     2022-10-09 [1] Bioconductor
#>  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)
#>  lattice                0.20-45    2021-09-22 [3] CRAN (R 4.2.1)
#>  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)
#>  Matrix                 1.5-1      2022-09-13 [2] RSPM (R 4.2.0)
#>  MatrixGenerics       * 1.9.1      2022-06-24 [1] Bioconductor
#>  matrixStats          * 0.62.0     2022-04-19 [1] RSPM (R 4.2.0)
#>  memoise                2.0.1      2021-11-26 [2] RSPM (R 4.2.0)
#>  pkgdown                2.0.6.9000 2022-10-09 [1] Github (r-lib/pkgdown@7fe9e80)
#>  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)
#>  RCurl                  1.98-1.9   2022-10-03 [1] 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              2.16       2022-08-24 [2] RSPM (R 4.2.0)
#>  rprojroot              2.0.3      2022-04-02 [2] RSPM (R 4.2.0)
#>  S4Vectors            * 0.35.4     2022-09-18 [1] Bioconductor
#>  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)
#>  SummarizedExperiment * 1.27.3     2022-09-13 [1] Bioconductor
#>  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                   0.33       2022-09-12 [2] RSPM (R 4.2.0)
#>  xml2                   1.3.3      2021-11-30 [2] RSPM (R 4.2.0)
#>  XVector                0.37.1     2022-08-25 [1] Bioconductor
#>  yaml                   2.3.5      2022-02-21 [2] RSPM (R 4.2.0)
#>  zlibbioc               1.43.0     2022-04-26 [1] Bioconductor
#> 
#>  [1] /__w/_temp/Library
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/local/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Bibliography

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 2.16. 2022. URL: https://github.com/rstudio/rmarkdown.

[2] iSEE. Demonstration of a Bioconductor Package. https://github.com/iSEE/iSEEGenerics/iSEEGenerics - R package version 0.99.0. 2022. DOI: 10.18129/B9.bioc.iSEEGenerics. URL: http://www.bioconductor.org/packages/iSEEGenerics.

[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/.

Kevin Rue-Albrecht

9 October 2022

Basics

Install `iSEEGenerics`

Required knowledge

Asking for help

Citing `iSEEGenerics`

Quick start to using to `iSEEGenerics`

Reproducibility

Bibliography

Introduction to iSEEGenerics

Kevin Rue-Albrecht

9 October 2022

Basics

Install iSEEGenerics

Required knowledge

Asking for help

Citing iSEEGenerics

Quick start to using to iSEEGenerics

Reproducibility

Bibliography

Install `iSEEGenerics`

Citing `iSEEGenerics`

Quick start to using to `iSEEGenerics`