synaptome.data 0.99.6
Genes encoding synaptic proteins are highly associated with neuronal disorders, many of which show clinical co-morbidity. Authors of (Sorokina, Mclean, Croning, Heil, Wysocka, He, Sterratt, Grant, Simpson, and Armstrong, 2021) integrated 58 published synaptic proteomic datasets that describe over 8000 proteins. They combined protein datasets with direct protein-protein interactions and functional metadata to build a database. Analysis of that database reveals the shared and unique protein components that underpin multiple disorders. The synaptome.data provides Bioconductor with access to the public version of that database .
synaptome.dataR is an open-source statistical environment which can be easily modified to enhance its functionality via packages. synaptome.data 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 synaptome.data by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("synaptome.data")
## Check that you have a valid Bioconductor installation
BiocManager::valid()synaptome.data 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.
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 synaptome.data 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.
synaptome.dataWe hope that synaptome.data will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("synaptome.data")
#>
#> To cite synaptome.db in publications use:
#>
#> Sorokina, O., Mclean, C., Croning, M.D.R. et al. A unified resource
#> and configurable model of the synapse proteome and its role in
#> disease. Sci Rep 11, 9967 (2021).
#> https://doi.org/10.1038/s41598-021-88945-7
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {A unified resource and configurable model of the synapse proteome and its role in disease},
#> author = {Oksana Sorokina and Colin Mclean and Mike D. R. Croning and Katharina F. Heil and Emilia Wysocka and Xin He and David Sterratt and Seth G. N. Grant and T. Ian Simpson and J. Douglas Armstrong},
#> journal = {Scientific Reports},
#> year = {2021},
#> volume = {11},
#> number = {1},
#> pages = {9967},
#> doi = {10.1038/s41598-021-88945-7},
#> url = {https://doi.org/10.1038/s41598-021-88945-7},
#> }synaptome.datalibrary("synaptome.data")
ahub <- AnnotationHub::AnnotationHub(hub='http://127.0.0.1:9393/')
sdb<-AnnotationHub::query(ahub,'SynaptomeDB')Here is an example of you can cite your package inside the vignette:
The synaptome.data package (Sorokina, Mclean, Croning et al., 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("data_vignette.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("data_vignette.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2022-10-19 03:02:23 EDT"Wallclock time spent generating the vignette.
#> Time difference of 0.509 secsR 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 C
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2022-10-19
#> pandoc 2.5 @ /usr/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [2] CRAN (R 4.2.1)
#> bibtex 0.5.0 2022-09-25 [2] CRAN (R 4.2.1)
#> BiocManager 1.30.18 2022-05-18 [2] CRAN (R 4.2.1)
#> BiocStyle * 2.25.0 2022-10-18 [2] Bioconductor
#> bookdown 0.29 2022-09-12 [2] CRAN (R 4.2.1)
#> bslib 0.4.0 2022-07-16 [2] CRAN (R 4.2.1)
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#> cli 3.4.1 2022-09-23 [2] CRAN (R 4.2.1)
#> digest 0.6.30 2022-10-18 [2] CRAN (R 4.2.1)
#> evaluate 0.17 2022-10-07 [2] CRAN (R 4.2.1)
#> fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.2.1)
#> generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.1)
#> htmltools 0.5.3 2022-07-18 [2] CRAN (R 4.2.1)
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#> jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.2.1)
#> jsonlite 1.8.2 2022-10-02 [2] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [2] CRAN (R 4.2.1)
#> lubridate 1.8.0 2021-10-07 [2] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.1)
#> plyr 1.8.7 2022-03-24 [2] CRAN (R 4.2.1)
#> R6 2.5.1 2021-08-19 [2] CRAN (R 4.2.1)
#> Rcpp 1.0.9 2022-07-08 [2] CRAN (R 4.2.1)
#> RefManageR * 1.4.0 2022-09-30 [2] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [2] CRAN (R 4.2.1)
#> rmarkdown 2.17 2022-10-07 [2] CRAN (R 4.2.1)
#> sass 0.4.2 2022-07-16 [2] CRAN (R 4.2.1)
#> sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.2.1)
#> stringi 1.7.8 2022-07-11 [2] CRAN (R 4.2.1)
#> stringr 1.4.1 2022-08-20 [2] CRAN (R 4.2.1)
#> xfun 0.33 2022-09-12 [2] CRAN (R 4.2.1)
#> xml2 1.3.3 2021-11-30 [2] CRAN (R 4.2.1)
#> yaml 2.3.6 2022-10-18 [2] CRAN (R 4.2.1)
#>
#> [1] /tmp/RtmpWRZ2Jl/Rinst1e59c129973f0d
#> [2] /home/biocbuild/bbs-3.16-bioc/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────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 2.17. 2022. 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 2.25.0. 2022. URL: https://github.com/Bioconductor/BiocStyle.
[4] 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/.
[5] O. Sorokina, C. Mclean, M. D. R. Croning, et al. “A unified resource and configurable model of the synapse proteome and its role in disease”. In: Scientific Reports 11.1 (2021), p. 9967. DOI: 10.1038/s41598-021-88945-7. URL: https://doi.org/10.1038/s41598-021-88945-7.
[6] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.2. 2021. URL: https://CRAN.R-project.org/package=sessioninfo.
[7] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.40. 2022. URL: https://yihui.org/knitr/.