## ----loadLibs, eval=FALSE-------------------------------------------------- # source("http://www.bioconductor.org/biocLite.R") # biocLite('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="50%", echo=FALSE---------------------------- knitr::include_graphics("denbi_logo.jpg")