Access GSE159526 data using Bioconductor’s ExperimentHub

How to access GSE159526 with Bioconductor

Citing GSE159526

We hope that GSE159526 will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("GSE159526")
#> To cite package 'GSE159526' in publications use:
#> 
#>   Yuan V, Hui D, Penaherrera M, Beristain A, Robinson W (2021).
#>   "Cell-specific characterization of the placental methylome." _BMC
#>   Genomics_. doi:10.1186/s12864-020-07186-6
#>   <https://doi.org/10.1186/s12864-020-07186-6>.
#>   <https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07186-6>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Cell-specific characterization of the placental methylome},
#>     author = {Victor Yuan and Desmond Hui and Maria S. Penaherrera and Alexander G. Beristain and Wendy P. Robinson},
#>     year = {2021},
#>     journal = {BMC Genomics},
#>     doi = {10.1186/s12864-020-07186-6},
#>     url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07186-6},
#>   }

Quick start to using to GSE159526

There are 3 objects associated with GSE159526:

EH6130 - Raw DNA methylation data, .idat files read into r with minfi and saved as an rgset object.

EH6131 - Processed filtered DNA methylation data. Described in (Yuan, Hui, Penaherrera, Beristain, and Robinson, 2021).

EH6132 - Sample information stored as a tibble/data.frame object.

eh <- ExperimentHub()
query(eh, "GSE159526")

# raw rgset
library(minfi)
GSE159526_rgset <- eh[['EH6130']] # requires minfi

# normalized processed data matrix
GSE159526_data <- eh[['EH6131']]

# sample information
GSE159526_pdat <- eh[['EH6132']]

Reproducibility

The GSE159526 package (Yuan, Hui, Penaherrera et al., 2021) was made possible thanks to:

  • R (R Core Team, 2026)
  • BiocStyle (Oleś, 2026)
  • knitr (Xie, 2026)
  • 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.

Code for creating the vignette:

## Create the vignette
library("rmarkdown")
system.time(render(here::here("vignettes", "GSE159526.Rmd"), 
                   "BiocStyle::html_document"))

## Extract the R code
library("knitr")
knit("GSE159526.Rmd", tangle = TRUE)

Date the vignette was generated.

#> [1] "2026-10-10 11:15:23 UTC"

Wallclock time spent generating the vignette.

#> Time difference of 0.553 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.6.1 (2026-06-24)
#>  os       Ubuntu 26.04.1 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Etc/UTC
#>  date     2026-10-10
#>  pandoc   3.8.3 @ /usr/local/bin/ (via rmarkdown)
#>  quarto   1.9.37 @ /usr/local/bin/quarto
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  bibtex        0.5.3   2026-09-22 [2] RSPM (R 4.6.0)
#>  BiocManager   1.30.27 2025-11-14 [2] RSPM (R 4.6.0)
#>  BiocStyle   * 2.40.0  2026-04-28 [2] Bioconductor 3.23 (R 4.6.1)
#>  bslib         0.12.0  2026-08-04 [2] RSPM (R 4.6.0)
#>  buildtools    1.0.0   2026-10-10 [3] local (/pkg)
#>  cachem        1.1.0   2024-05-16 [2] RSPM (R 4.6.0)
#>  cli           3.6.6   2026-04-09 [2] RSPM (R 4.6.0)
#>  digest        0.6.39  2025-11-19 [2] RSPM (R 4.6.0)
#>  evaluate      1.0.5   2025-08-27 [2] RSPM (R 4.6.0)
#>  fastmap       1.2.0   2024-05-15 [2] RSPM (R 4.6.0)
#>  generics      0.1.4   2025-05-09 [2] RSPM (R 4.6.0)
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#>  htmltools     0.5.9   2025-12-04 [2] RSPM (R 4.6.0)
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#>  jquerylib     0.1.4   2021-04-26 [2] RSPM (R 4.6.0)
#>  jsonlite      2.0.0   2025-03-27 [2] RSPM (R 4.6.0)
#>  knitr         1.52    2026-09-06 [2] RSPM (R 4.6.0)
#>  lifecycle     1.0.5   2026-01-08 [2] RSPM (R 4.6.0)
#>  lubridate     1.9.5   2026-02-04 [2] RSPM (R 4.6.0)
#>  magrittr      2.0.5   2026-04-04 [2] RSPM (R 4.6.0)
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#>  plyr          1.8.9   2023-10-02 [2] RSPM (R 4.6.0)
#>  R6            2.6.1   2025-02-15 [2] RSPM (R 4.6.0)
#>  Rcpp          1.1.2   2026-07-05 [2] RSPM (R 4.6.0)
#>  RefManageR  * 1.4.0   2022-09-30 [2] RSPM (R 4.6.0)
#>  rlang         1.3.0   2026-07-05 [2] RSPM (R 4.6.0)
#>  rmarkdown     2.32    2026-09-01 [2] RSPM (R 4.6.0)
#>  sass          0.4.10  2025-04-11 [2] RSPM (R 4.6.0)
#>  sessioninfo * 1.2.4   2026-06-04 [2] RSPM (R 4.6.0)
#>  stringi       1.8.9   2026-08-04 [2] RSPM (R 4.6.0)
#>  stringr       1.6.0   2025-11-04 [2] RSPM (R 4.6.0)
#>  sys           3.4.3   2024-10-04 [2] RSPM (R 4.6.0)
#>  timechange    0.4.0   2026-01-29 [2] RSPM (R 4.6.0)
#>  xfun          0.61    2026-09-16 [2] RSPM (R 4.6.0)
#>  xml2          1.6.0   2026-06-22 [2] RSPM (R 4.6.0)
#>  yaml          2.3.12  2025-12-10 [2] RSPM (R 4.6.0)
#> 
#>  [1] /tmp/RtmpWQenp3/Rinst1a262d1bb56
#>  [2] /github/workspace/pkglib
#>  [3] /usr/local/lib/R/site-library
#>  [4] /usr/lib/R/site-library
#>  [5] /usr/lib/R/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Bibliography

This vignette was generated using BiocStyle (Oleś, 2026) with knitr (Xie, 2026) 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 2.32. 2026. 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 2.40.0. 2026. URL: https://github.com/Bioconductor/BiocStyle.

[4] 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/.

[5] 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/.

[6] 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.

[7] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.52. 2026. URL: https://yihui.org/knitr/.

[8] V. Yuan, D. Hui, M. Penaherrera, et al. “Cell-specific characterization of the placental methylome”. In: BMC Genomics (2021). DOI: 10.1186/s12864-020-07186-6. URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07186-6.