vignettes/visiumStitched.Rmd
visiumStitched.RmdvisiumStitched
visiumStitched
is a R package available from GitHub. It
can be installed with the following commands in your R
session:
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install("LieberInstitute/visiumStitched")For now, visiumStitched doesn’t have a demonstrative vignette as documentation. Please refer to the Reference for info about how to use its functions, and examples.
visiumStitched
We hope that visiumStitched will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("visiumStitched")
#> To cite package 'visiumStitched' in publications use:
#>
#> Eagles N (2024). _visiumStitched: Helper package for working with
#> stitched overlapping Visium capture areas_. R package version 0.99.0,
#> <https://github.com/LieberInstitute/visiumStitched>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {visiumStitched: Helper package for working with stitched overlapping Visium capture areas},
#> author = {Nicholas J. Eagles},
#> year = {2024},
#> note = {R package version 0.99.0},
#> url = {https://github.com/LieberInstitute/visiumStitched},
#> }The visiumStitched package (Eagles, 2024) was made possible thanks to:
This package was developed using biocthis.
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("visiumStitched.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("visiumStitched.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2024-06-06 17:41:22 UTC"Wallclock time spent generating the vignette.
#> Time difference of 0.702 secsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.0 (2024-04-24)
#> os Ubuntu 22.04.4 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2024-06-06
#> pandoc 3.2 @ /usr/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.5.0 2024-05-23 [1] RSPM (R 4.4.0)
#> bibtex 0.5.1 2023-01-26 [1] RSPM (R 4.4.0)
#> BiocManager 1.30.23 2024-05-04 [2] CRAN (R 4.4.0)
#> BiocStyle * 2.33.0 2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
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#> glue 1.7.0 2024-01-09 [2] RSPM (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.4.0)
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#> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.4.0)
#> pkgdown 2.0.9.9000 2024-06-06 [1] Github (r-lib/pkgdown@0e1352c)
#> plyr 1.8.9 2023-10-02 [1] RSPM (R 4.4.0)
#> R6 2.5.1 2021-08-19 [2] RSPM (R 4.4.0)
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#> Rcpp 1.0.12 2024-01-09 [2] RSPM (R 4.4.0)
#> RefManageR * 1.4.0 2022-09-30 [1] RSPM (R 4.4.0)
#> rlang 1.1.4 2024-06-04 [2] RSPM (R 4.4.0)
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#> sessioninfo * 1.2.2 2021-12-06 [2] RSPM (R 4.4.0)
#> stringi 1.8.4 2024-05-06 [2] RSPM (R 4.4.0)
#> stringr 1.5.1 2023-11-14 [2] RSPM (R 4.4.0)
#> systemfonts 1.1.0 2024-05-15 [2] RSPM (R 4.4.0)
#> textshaping 0.4.0 2024-05-24 [2] RSPM (R 4.4.0)
#> timechange 0.3.0 2024-01-18 [1] RSPM (R 4.4.0)
#> xfun 0.44 2024-05-15 [2] RSPM (R 4.4.0)
#> xml2 1.3.6 2023-12-04 [2] RSPM (R 4.4.0)
#> yaml 2.3.8 2023-12-11 [2] RSPM (R 4.4.0)
#>
#> [1] /__w/_temp/Library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/local/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────This vignette was generated using BiocStyle (Oleś, 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 2.27. 2024. URL: https://github.com/rstudio/rmarkdown.
[2] N. Eagles. visiumStitched: Helper package for working with stitched overlapping Visium capture areas. R package version 0.99.0. 2024. URL: https://github.com/LieberInstitute/visiumStitched.
[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 2.33.0. 2024. 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, 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 1.47. 2024. URL: https://yihui.org/knitr/.