vignettes/spoar.Rmd
spoar.Rmdspoar
R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. spoar 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 spoar by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("spoar")
## Check that you have a valid Bioconductor installation
BiocManager::valid()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 spoar 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.
spoar
We hope that spoar will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("spoar")
#>
#> Furneaux B, Vaser R (2021). _SPOAR: SIMD Partial Order Alignment in R_.
#> doi: 10.18129/B9.bioc.spoar (URL:
#> https://doi.org/10.18129/B9.bioc.spoar),
#> https://github.com/brendanf/spoar/spoar - R package version 0.99.3,
#> <URL: http://www.bioconductor.org/packages/spoar>.
#>
#> Vaser R, Sović I, Nagaranjan N, Šikić M (2017). "Fast and accurate de
#> novo genome assembly from long uncorrected reads." _Genome Research_,
#> *27*, 737-746. doi: 10.1101/gr.214270.116 (URL:
#> https://doi.org/10.1101/gr.214270.116), <URL:
#> https://doi.org/10.1101/gr.214270.116>.
#>
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.spoar
Edit this as you see fit =)
Here is an example of you can cite your package inside the vignette:
The spoar package (Furneaux and Vaser, 2021) was made possible thanks to:
This package was developed using biocthis.
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("spoar.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("spoar.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2021-05-17 21:22:31 UTC"Wallclock time spent generating the vignette.
#> Time difference of 1.138 secsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.3 (2020-10-10)
#> os Ubuntu 20.04 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Etc/UTC
#> date 2021-05-17
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [2] RSPM (R 4.0.3)
#> BiocManager 1.30.10 2019-11-16 [1] RSPM (R 4.0.0)
#> BiocStyle * 2.18.1 2020-11-24 [1] Bioconductor
#> bookdown 0.21 2020-10-13 [1] RSPM (R 4.0.2)
#> cachem 1.0.4 2021-02-13 [2] RSPM (R 4.0.3)
#> cli 2.3.0 2021-01-31 [2] RSPM (R 4.0.3)
#> crayon 1.4.1 2021-02-08 [2] RSPM (R 4.0.3)
#> desc 1.2.0 2018-05-01 [2] RSPM (R 4.0.3)
#> digest 0.6.27 2020-10-24 [2] RSPM (R 4.0.3)
#> evaluate 0.14 2019-05-28 [2] RSPM (R 4.0.3)
#> fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.0.3)
#> fs 1.5.0 2020-07-31 [2] RSPM (R 4.0.3)
#> generics 0.1.0 2020-10-31 [1] RSPM (R 4.0.3)
#> glue 1.4.2 2020-08-27 [2] RSPM (R 4.0.3)
#> htmltools 0.5.1.1 2021-01-22 [2] RSPM (R 4.0.3)
#> httr 1.4.2 2020-07-20 [2] RSPM (R 4.0.3)
#> jsonlite 1.7.2 2020-12-09 [2] RSPM (R 4.0.3)
#> knitr 1.31 2021-01-27 [2] RSPM (R 4.0.3)
#> lubridate 1.7.9.2 2020-11-13 [1] RSPM (R 4.0.3)
#> magrittr 2.0.1 2020-11-17 [2] RSPM (R 4.0.3)
#> memoise 2.0.0 2021-01-26 [2] RSPM (R 4.0.3)
#> pkgdown 1.6.1 2020-09-12 [1] RSPM (R 4.0.2)
#> plyr 1.8.6 2020-03-03 [1] RSPM (R 4.0.3)
#> R6 2.5.0 2020-10-28 [2] RSPM (R 4.0.3)
#> ragg 1.1.0 2021-02-15 [1] RSPM (R 4.0.3)
#> Rcpp 1.0.6 2021-01-15 [2] RSPM (R 4.0.3)
#> RefManageR * 1.3.0 2020-11-13 [1] RSPM (R 4.0.3)
#> rlang 0.4.10 2020-12-30 [2] RSPM (R 4.0.3)
#> rmarkdown 2.6 2020-12-14 [1] RSPM (R 4.0.3)
#> rprojroot 2.0.2 2020-11-15 [2] RSPM (R 4.0.3)
#> sessioninfo * 1.1.1 2018-11-05 [2] RSPM (R 4.0.3)
#> spoar * 0.99.3 2021-05-17 [1] Bioconductor
#> stringi 1.5.3 2020-09-09 [2] RSPM (R 4.0.3)
#> stringr 1.4.0 2019-02-10 [2] RSPM (R 4.0.3)
#> systemfonts 1.0.1 2021-02-09 [1] RSPM (R 4.0.3)
#> textshaping 0.3.0 2021-02-10 [1] RSPM (R 4.0.3)
#> withr 2.4.1 2021-01-26 [2] RSPM (R 4.0.3)
#> xfun 0.21 2021-02-10 [2] RSPM (R 4.0.3)
#> xml2 1.3.2 2020-04-23 [2] RSPM (R 4.0.3)
#> yaml 2.2.1 2020-02-01 [2] RSPM (R 4.0.3)
#>
#> [1] /__w/_temp/Library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/local/lib/R/libraryThis vignette was generated using BiocStyle (Oleś, Morgan, and Huber, 2020) with knitr (Xie, 2021) and rmarkdown (Allaire, Xie, McPherson, et al., 2020) 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 2.6. 2020. URL: https://github.com/rstudio/rmarkdown.
[2] G. Csárdi, R. core, H. Wickham, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. URL: https://github.com/r-lib/sessioninfo#readme.
[3] B. Furneaux and R. Vaser. SPOAR: SIMD Partial Order Alignment in R. https://github.com/brendanf/spoar/spoar - R package version 0.99.3. 2021. DOI: 10.18129/B9.bioc.spoar. URL: http://www.bioconductor.org/packages/spoar.
[4] 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.
[5] A. Oleś, M. Morgan, and W. Huber. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.18.1. 2020. URL: https://github.com/Bioconductor/BiocStyle.
[6] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2020. URL: https://www.R-project.org/.
[7] 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.
[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.31. 2021. URL: https://yihui.org/knitr/.