Introduction to cosexpressionR
Juliana Costa-Silva
Federal University of Paraná - UFPR and Federal Technological University of Paraná (UTFPR)julianacostasilvati@gmail.com
23 June 2026
Source:vignettes/consexpressionR.Rmd
consexpressionR.RmdBasics
Install consexpressionR
R is an open-source statistical environment which can be
easily modified to enhance its functionality via packages. consexpressionR
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
consexpressionR
by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("consexpressionR")
## Check that you have a valid Bioconductor installation
BiocManager::valid()Required knowledge
consexpressionR 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
consexpressionR 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 consexpressionR
We hope that consexpressionR will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("consexpressionR")
#> To cite package 'consexpressionR' in publications use:
#>
#> Costa-Silva, J., Menotti, D., Lopes, M. F. consexpressionR: an R
#> package for consensus differential gene expression analysis arxiv
#> (2025)
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {consexpressionR: an R package for consensus differential gene expression analysis},
#> author = {Juliana Costa-Silva and David Menotti and Fabricio M. Lopes},
#> year = {2025},
#> journal = {arxiv},
#> doi = {10.48550/arXiv.2503.21546},
#> }Quick start to using consexpressionR
Edit this as you see fit =)
Here is an example of you can cite your package inside the vignette:
- consexpressionR (Costa-Silva, Menotti, and Lopes, 2025)
Reproducibility
The consexpressionR package (Costa-Silva, Menotti, and Lopes, 2025) was made possible thanks to:
- R (R Core Team, 2026)
- BiocStyle (Oleś, 2026)
- knitr (Xie, 2025)
- RefManageR (McLean, 2017)
- rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2026)
- sessioninfo (Wickham, Chang, Flight, Müller, and Hester, 2026)
- testthat (Wickham, 2011)
This package was developed using biocthis.
R session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.6.0 (2026-04-24)
#> os Ubuntu 24.04.4 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en
#> collate C.UTF-8
#> ctype C.UTF-8
#> tz UTC
#> date 2026-06-23
#> pandoc 3.8.3 @ /opt/hostedtoolcache/pandoc/3.8.3/x64/ (via rmarkdown)
#> quarto NA
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.5.1 2026-04-03 [1] RSPM
#> bibtex 0.5.2 2026-02-03 [1] RSPM
#> BiocManager 1.30.27 2025-11-14 [1] RSPM
#> BiocStyle * 2.40.0 2026-04-28 [1] Bioconduc~
#> bookdown 0.47 2026-06-16 [1] RSPM
#> bslib 0.11.0 2026-05-16 [1] RSPM
#> cachem 1.1.0 2024-05-16 [1] RSPM
#> cli 3.6.6 2026-04-09 [1] RSPM
#> consexpressionR * 0.99.0 2026-06-23 [1] local
#> desc 1.4.3 2023-12-10 [1] RSPM
#> digest 0.6.39 2025-11-19 [1] RSPM
#> evaluate 1.0.5 2025-08-27 [1] RSPM
#> fastmap 1.2.0 2024-05-15 [1] RSPM
#> fs 2.1.0 2026-04-18 [1] RSPM
#> generics 0.1.4 2025-05-09 [1] RSPM
#> glue 1.8.1 2026-04-17 [1] RSPM
#> htmltools 0.5.9 2025-12-04 [1] RSPM
#> htmlwidgets 1.6.4 2023-12-06 [1] RSPM
#> httr 1.4.8 2026-02-13 [1] RSPM
#> jquerylib 0.1.4 2021-04-26 [1] RSPM
#> jsonlite 2.0.0 2025-03-27 [1] RSPM
#> knitr 1.51 2025-12-20 [1] RSPM
#> lifecycle 1.0.5 2026-01-08 [1] RSPM
#> lubridate 1.9.5 2026-02-04 [1] RSPM
#> magrittr 2.0.5 2026-04-04 [1] RSPM
#> otel 0.2.0 2025-08-29 [1] RSPM
#> pkgdown 2.2.0 2025-11-06 [1] RSPM
#> plyr 1.8.9 2023-10-02 [1] RSPM
#> R6 2.6.1 2025-02-15 [1] RSPM
#> ragg 1.5.2 2026-03-23 [1] RSPM
#> Rcpp 1.1.1-1.1 2026-04-24 [1] RSPM
#> RefManageR * 1.4.0 2022-09-30 [1] RSPM
#> rlang 1.2.0 2026-04-06 [1] RSPM
#> rmarkdown 2.31 2026-03-26 [1] RSPM
#> sass 0.4.10 2025-04-11 [1] RSPM
#> sessioninfo * 1.2.4 2026-06-04 [1] RSPM
#> stringi 1.8.7 2025-03-27 [1] RSPM
#> stringr 1.6.0 2025-11-04 [1] RSPM
#> systemfonts 1.3.2 2026-03-05 [1] RSPM
#> textshaping 1.0.5 2026-03-06 [1] RSPM
#> timechange 0.4.0 2026-01-29 [1] RSPM
#> xfun 0.59 2026-06-19 [1] RSPM
#> xml2 1.6.0 2026-06-22 [1] RSPM
#> yaml 2.3.12 2025-12-10 [1] RSPM
#>
#> [1] /home/runner/work/_temp/Library
#> [2] /opt/R/4.6.0/lib/R/site-library
#> [3] /opt/R/4.6.0/lib/R/library
#> * ── Packages attached to the search path.
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────Bibliography
This vignette was generated using BiocStyle (Oleś, 2026) with knitr (Xie, 2025) and rmarkdown (Allaire, Xie, Dervieux et al., 2026) 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 2.31. 2026. URL: https://github.com/rstudio/rmarkdown.
[2] J. Costa-Silva, D. Menotti, and F. M. Lopes. “consexpressionR: an R package for consensus differential gene expression analysis”. In: arxiv (2025). DOI: 10.48550/arXiv.2503.21546.
[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 2.40.0. 2026. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.
[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing (ROR: <https://ror.org/05qewa988>;). Vienna, Austria, 2026. DOI: 10.32614/R.manuals. 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/articles/RJ-2011-002/.
[7] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.4. 2026. URL: https://sessioninfo.r-lib.org.
[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.51. 2025. URL: https://yihui.org/knitr/.