In lcolladotor/biocthis: Automate package and project setup for Bioconductor packages

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html
)

## Track time spent on making the vignette
startTime <- Sys.time()

## Bib setup
library("RefManageR")

## Write bibliography information
bib <- c(
    R = citation(),
    BiocStyle = citation("BiocStyle")[1],
    knitr = citation("knitr")[1],
    RefManageR = citation("RefManageR")[1],
    rmarkdown = citation("rmarkdown")[1],
    sessioninfo = citation("sessioninfo")[1],
    testthat = citation("testthat")[1],
    {{ Package }} = citation("{{ Package }}")[1]
)

Basics

Install {{ Package }}

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. r Biocpkg("{{ Package }}") 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 r Biocpkg("{{ Package }}") by using the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
  }

BiocManager::install("{{ Package }}")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

Required knowledge

r Biocpkg("{{ Package }}") 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 r Biocpkg("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 {{ Package }} 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 {{ Package }}

We hope that r Biocpkg("{{ Package }}") will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("{{ Package }}")

Quick start to using {{ Package }}

library("{{ Package }}")

Edit this as you see fit =)

Here is an example of you can cite your package inside the vignette:

• r Biocpkg("{{ Package }}") r Citep(bib[["{{ Package }}"]])

Reproducibility

The r Biocpkg("{{ Package }}") package r Citep(bib[["{{ Package }}"]]) was made possible thanks to:

• R r Citep(bib[["R"]])
• r Biocpkg("BiocStyle") r Citep(bib[["BiocStyle"]])
• r CRANpkg("knitr") r Citep(bib[["knitr"]])
• r CRANpkg("RefManageR") r Citep(bib[["RefManageR"]])
• r CRANpkg("rmarkdown") r Citep(bib[["rmarkdown"]])
• r CRANpkg("sessioninfo") r Citep(bib[["sessioninfo"]])
• r CRANpkg("testthat") r Citep(bib[["testthat"]])

This package was developed using r BiocStyle::Biocpkg("biocthis").

Code for creating the vignette

## Create the vignette
library("rmarkdown")
system.time(render("{{ vignette_name }}.Rmd", "BiocStyle::html_document"))

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

Date the vignette was generated.

## Date the vignette was generated
Sys.time()

Wallclock time spent generating the vignette.

## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)

R session information.

## Session info
library("sessioninfo")
options(width = 120)
session_info()

Bibliography

This vignette was generated using r Biocpkg("BiocStyle") r Citep(bib[["BiocStyle"]]) with r CRANpkg("knitr") r Citep(bib[["knitr"]]) and r CRANpkg("rmarkdown") r Citep(bib[["rmarkdown"]]) running behind the scenes.

Citations made with r CRANpkg("RefManageR") r Citep(bib[["RefManageR"]]).

## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))

lcolladotor/biocthis documentation built on Jan. 17, 2024, 8:07 p.m.