README.Rmd

---
output: github_document
---

# bcbioR

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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.

## Installation

You can install the development version of bcbioR from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("bcbio/bcbioR")
```

## Quick start

``` r
library(bcbioR)
## basic example code
# will help you to build a folder name following HCBC naming rules
bcbio_set_project()
```

### Set base project

The following code will pop up a Rmd template and then clicking 'save' will populate that folder with HCBC data structure guidelines

``` r
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

### Set RNAseq report folder

This code will populate the folder with HCBC data structure guidelines and Rmd code:

``` r
bcbio_templates(type="rnaseq", outpath="test_folder/reports")
```

### Discover more...

Go to the vignette to know more `vignette("bcbioR_quick_start,package="bcbioR")`

## How to Contribute

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.

### Contributors

-   Lorena Pantano
-   Alex Bartlett
-   Emma Berdan
-   Heather Wick
-   James Billingsley