The goal of bcbioR is to create guidelines for NGS data interpretation
based on the experience of the Harvard Chan Bioinformatics Core and
everybody who contributes to this package.
You can install the development version of bcbioR from GitHub with:
# install.packages("devtools")
devtools::install_github("bcbio/bcbioR")library(bcbioR)
## basic example code
# will help you to build a folder name following HCBC naming rules
bcbio_set_project()The following code will pop up a Rmd template and then clicking ‘save’ will populate that folder with HCBC data structure guidelines
rmarkdown::draft("project_folder",template="common",package="bcbioR")As well, You can get this by going to File -> New File -> R
markdown: - then From Template, and choose bcbio base - choose the
folder to deploy files, it could be a new folder or an existing one
This code will populate the folder with HCBC data structure guidelines and Rmd code:
bcbio_templates(type="rnaseq", outpath="test_folder/reports")Go to the vignette to know more
vignette("bcbioR_quick_start,package="bcbioR")
You’ll still need to render README.Rmd regularly, to keep README.md
up-to-date. devtools::build_readme() is handy for this.
Use usethis::use_import_from("stringr","str_replace_all") to add a
function you are using in the code.
Don’t forget to commit and push the resulting figure files, so they display on GitHub and CRAN.
- Lorena Pantano
- Alex Bartlett
- Emma Berdan
- Heather Wick
- James Billingsley