Getting Started with pepr

Nathan Sheffield

2026-02-28

Introduction to pepr

pepr is the official R package for the pepkit suite, a collection of tools that interface with portable encapsulated projects, or PEPs. PEP format defines a structure for organizing project metadata using a yaml file. pepr allows you to read any PEP-formatted project metadata (and potentially even actual sample data) into R, providing you a convenient user interface to interact with and share project metadata.

Installing pepr

You can install pepr in the usual way. Currently from GitHub (but we target a CRAN release at some point).

devtools::install_github('pepkit/pepr')

Loading an example project

Load pepr and read in your project. We have provided a basic example to show you how it works. You can use this to get the file path to a built-in example project configuration yaml file:

library('pepr')
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
branch = "master"
projectConfigFile = system.file("extdata",
    paste0("example_peps-", branch),
    "example_basic",
    "project_config.yaml",
    package="pepr")

Loading your project metadata into R is a single line of code:

p = pepr::Project(file=projectConfigFile)

## Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml

That’s it! You now have a Project object, p, to interact with in R. You can also use PEPhub registry paths to fetch them online:

p2 = pepr::pullProject(registryPath='databio/example:default')

## Warning in fetchPEP(ellipsis$file, raw = TRUE): No authentication token found.
## Generate one with PEPhub Client to access private PEPs.

To fetch private PEPs, use PEPhub Client to login and generate an authentication token. Or, login to PEPhub and generate a new key to save it locally:

pepr::saveJWT('*your authetication token goes here*')

You should then be able to fetch your private PEPs by registry path.

Interfacing with your pepr::Project object in R

Now you can interface with that project object to grab both sample-level and project-level metadata. Here’s how you can access the metadata. If you just run the show() function on your object, you’ll get a simple report telling you a few basic stats, like where the project came from and how many samples it has:

p

## PEP project object. Class:  Project
##   file:  
## /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml
##   samples:  2

To get the sample table out of the project, you use the samples() function:

sampleTable(p)
##    sample_name      protocol                file
##         <char>        <char>              <char>
## 1:      frog_1 anySampleType data/frog1_data.txt
## 2:      frog_2 anySampleType data/frog2_data.txt

And you can also access the project configuration metadata with the config() function:

config(p)

## Config object. Class: Config
## pep_version: 2.0.0
## sample_table: 
## /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/sample_table.csv
## name: example_basic

If you would like to save your project to a new directory, use the saveProject() function:

saveProject(p2, outputDir=tempdir())

## [1] TRUE

Follow the other vignettes for more advanced capabilities of pepr.