Reading Portable Encapsulated Projects

A PEP, or Portable Encapsulated Project, is a dataset that subscribes to the PEP structure for organizing metadata. It is written using a simple YAML + CSV format, it is your one-stop solution to metadata management across data analysis environments. This package reads this standardized project configuration structure into R. Described in Sheffield et al. (2021) .

The pepr package: Portable Encapsulated Projects in R

pepr is an R package for reading Portable Encapsulated Projects, or PEPs, in R. If you describe your project (configuration and samples) according to this format, you can load all project metadata into R using the pepr package. To test pepr, you can try loading one of the example PEPs.

Complete documentation and API for the pepr R package is at code.databio.org/pepr.

Quick start:

Install from CRAN:

install.packages("pepr")

Load a project and explore metadata like this:

library("pepr")
cfgPath = system.file(
    "extdata",
    "example_peps-master",
    "example_basic",
    "project_config.yaml",
    package = "pepr"
  )
p = Project(file = cfgPath)

sampleTable(p)
config(p)