bcbioR

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 with:

```

install.packages("devtools")

devtools::installgithub("bcbio/bcbioR") devtools::installgithub("bcbio/bcbioR",ref = "devel") ```

Quick start

Set base project

use setwd() to set your current directory to the place where you want to work. The bcbioR functions will automatically write to whatever directory you have set.

setwd("/path/to/analysis/folder")

The following code will pop up a Rmd template will populate that folder with HCBC data structure guidelines

path="/path/to/analysis/folder" bcbio_templates(type="base", outpath=path) bcbio_templates(type="rnaseq", outpath=path) bcbio_templates(type="singlecell", outpath=path)

Set RNAseq report folder

This code will populate the folder with HCBC data structure guidelines and Rmd code: You do not need to create a reports folder prior to running this code. This will create and populate the reports folder.

bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")

Supported analyses

• base/reports/example.Rmd:
• rnaseq-reports:
  • 01qualityassessment/QC.Rmd
  • 02differentialexpression/DEG.Rmd
  • 03functional/NonmodelOrganismPathwayAnalysis.Rmd
  • 03_functional/GSVA.Rmd
  • 03_functional/Immune-deconvolution.Rmd
  • 03_comparative/Pair-wise-comparison-analysis.Rmd:
  • 03_comparative/Intersections.Rmd
  • 04genepatterns/WGCNA.Rmd
  • 05genepatterns/DEGpattern.Rmd
• single-cell
  • singlecell/01qualityassessment/scRNA_QC.Rmd
  • 01qualityassessment/scATAC_QC.Rmd
  • 02differentialexpression/scRNA_MAST.Rmd
  • 02differentialexpression/scRNA_pseudobulk.Rmd
  • singlecell/04_compositional/propeller.Rmd
  • 04_compositional/sccomp.Rmd
  • 05_signaling/cellchat.Rmd:
• chipseq/02_diffbind/diffbind.Rmd:
• chipseq/01qualityassessment/QC.Rmd:
• spatial/visium/01qualityassessment/qc.Rmd:
• spatial/cosmx/01qualityassessment/QC.Rmd:

Discover more…

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

How to Contribute

Open an issue

• If you find a bug
• If you want a new feature
• If you want to add code to the templates

Modify the code

• Clone the repository
• Make sure you are in the devel branch
• Create a new branch git checkout -b feature1
• Modify you code, add and commit
• Push to GitHub the new branch
• Create a PR from your branch to devel
• Assignt the PR to me or Alex

Some best practices when developing:

• install devtools
• Use usethis::use_import_from("stringr","str_replace_all") to add a new function you are using in the code.

Contributors

• Lorena Pantano
• Alex Bartlett
• Emma Berdan
• Heather Wick
• James Billingsley
• Zhu Zhuo
• Elizabeth Partan
• Noor Sohail
• Meeta Mistry
• Will Gammerdinger
• Upen Bhattarai
• Shannan Ho Sui