## ----citation, eval = TRUE, echo = FALSE, results = 'asis'-------------------- print(citation('BiocWorkflowTools'), style = "HTML") ## ----loadLibs, eval=FALSE----------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install('BiocWorkflowTools') ## ----RStudioNew, echo = FALSE, out.width='90%', fig.align='center', fig.cap="Creation of a new article is integrated into RStudio. The F1000Research template can be accessed via the 'new R Markdown document' menu option."---- knitr::include_graphics("Rstudio_newdoc.png") ## ----createDraft-------------------------------------------------------------- tmp_dir <- tempdir() setwd(tmp_dir) rmarkdown::draft(file = "MyArticle.Rmd", template = "f1000_article", package = "BiocWorkflowTools", edit = FALSE) ## ----newFiles, echo = FALSE, out.width='90%', fig.align='center', fig.cap="The complete set of files. After 'knitting' both the LaTeX source file and PDF documents can be found alongside your Rmarkdown file."---- knitr::include_graphics("new_files.png") ## ----render, eval = FALSE----------------------------------------------------- # rmd_file <- file.path(tmp_dir, 'MyArticle', 'MyArticle.Rmd') # rmarkdown::render(input = rmd_file) ## ----upload, eval=FALSE------------------------------------------------------- # library(BiocWorkflowTools) # workflow_dir <- file.path(tmp_dir, 'MyArticle') # uploadToOverleaf(files = workflow_dir) ## ----sessionInfo, eval=TRUE--------------------------------------------------- sessionInfo() ## ----include_logo, out.width="60%", echo=FALSE-------------------------------- knitr::include_graphics("denbi_logo.jpg")