For example [rmarkdown](https://rmarkdown.rstudio.com/) is a great way to turn your analyses into high quality documents, reports, presentations and dashboards.
In addition most packages will provide **vignette**s on how to perform an analysis from scratch. On the [bioconductor.org](http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html) website (specialised on R packages for biologists), you will have direct links to the packages vignette.
Finally, don't forget to search the web for your problems or error in R websites like [stackoverflow](https://stackoverflow.com/) contains high quality and well-curated answers.