Package: pepr 0.6.1

Nathan Sheffield

pepr: 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) <doi:10.1093/gigascience/giab077>.

Authors:Nathan Sheffield [aut, cph, cre], Michal Stolarczyk [aut]

pepr_0.6.1.tar.gz
pepr_0.6.1.zip(r-4.7-any)pepr_0.6.1.zip(r-4.6-any)pepr_0.6.1.zip(r-4.5-any)
pepr_0.6.1.tgz(r-4.6-any)pepr_0.6.1.tgz(r-4.5-any)
pepr_0.6.1.tar.gz(r-4.7-any)pepr_0.6.1.tar.gz(r-4.6-any)
pepr_0.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pepr/json (API)

# Install 'pepr' in R:
install.packages('pepr', repos = c('https://pepkit.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pepkit/pepr/issues

On CRAN:

Conda:

bioinformaticslab-project-pepkitmetadata

6.25 score 3 stars 28 scripts 461 downloads 1 mentions 22 exports 19 dependencies

Last updated from:c48a6e6257. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK158
source / vignettesOK169
linux-releaseOK117
macos-releaseOK190
macos-oldrelOK154
windows-develOK75
windows-releaseOK86
windows-oldrelOK74
wasm-releaseOK102

Exports:.checkSection.expandList.expandPath.getSubscript.listifyDF.makeAbsPath.printNestedList.strformatactivateAmendmentscheckSectionconfigConfigfetchSamplesgetSamplegetSubsamplelistAmendmentsmakeSectionsAbsoluteProjectpullProjectsampleTablesaveJWTsaveProject

Dependencies:askpassbitopsclicurldata.tablegluehttr2lifecyclemagrittropensslR6RCurlrlangstringistringrsysvctrswithryaml

Amendments in pepr
Learn amendments in pepr | Problem/Goal | Solution | Code
Rendered fromfeature6_amendments.Rmdusingknitr::rmarkdown

Last update: 2026-02-28
Started: 2020-05-26

Getting Started with pepr
Introduction to pepr | Installing pepr | Loading an example project | Interfacing with your pepr::Project object in R
Rendered fromgettingStarted.Rmdusingknitr::rmarkdown

Last update: 2026-02-28
Started: 2017-10-26

Sample modifiers in pepr: append
Learn append sample modifier in pepr | Problem/Goal | Solution | Code
Rendered fromfeature1_constantAttributes.Rmdusingknitr::rmarkdown

Last update: 2026-02-28
Started: 2018-11-14

Sample modifiers in pepr: derive
Learn derived attributes in pepr | Problem/Goal | Solution | Code
Rendered fromfeature3_derivedAttributes.Rmdusingknitr::rmarkdown

Last update: 2026-02-28
Started: 2018-11-14

Sample modifiers in pepr: imply
Learn implied sample modifier in pepr | Problem/Goal | Solution | Code
Rendered fromfeature2_impliedAttributes.Rmdusingknitr::rmarkdown

Last update: 2026-02-28
Started: 2018-11-14

Subsample table in pepr
Learn sample subannotations in pepr | Problem/Goal | Solutions | Example 1: basic sample subannotation table | Example 2: subannotations and derived attributes | Example 3: subannotations and expansion characters | Example 4: subannotations and multiple (separate-class) inputs
Rendered fromfeature5_sampleSubtable.Rmdusingknitr::rmarkdown

Last update: 2026-02-28
Started: 2019-04-17

Sample modifiers in pepr: imply and derive
Learn how to combine implied and derived attributes in pepr | Problem/Goal | Solution | Code
Rendered fromfeature4_derivedImpliedAttributes.Rmdusingknitr::rmarkdown

Last update: 2023-11-17
Started: 2018-11-14

Readme and manuals

Help Manual

Help pageTopics
Activate amendments in objects of '"Project"'activateAmendments activateAmendments,Project,character-method
Check for existence of a section in the Project configcheckSection checkSection,Config-method
Extract '"Project"'config config,Project-method
Config objects and specialized list obejcts and expand string attributesConfig Config-class
Collect samples fulfilling the specified requirementsfetchSamples
Extract samplesgetSample getSample,Project,character-method
Extract subsamplesgetSubsample getSubsample,Project,character,character-method
List amendmentslistAmendments listAmendments,Project-method
Make selected sections absolute using config pathmakeSectionsAbsolute makeSectionsAbsolute,Config,character,character-method
peprpepr-package pepr
The constructor of a class representing a Portable Encapsulated ProjectProject
Portable Encapsulated Project objectProject-class
Pull a PEP from PEPhub APIpullProject
View samples in the objects of '"Project"'sampleTable sampleTable,Project-method
Save or update JWTsaveJWT
Save a modified PEP Project to a local directorysaveProject
Access '"Config"' object elements$,Config-method select-config [,Config-method [[,Config-method