Package: pepr 0.6.0

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_0.6.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
pepr/json (API)
NEWS

# 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:

bioinformaticsmetadata

5.80 score 3 stars 20 scripts 195 downloads 1 mentions 22 exports 20 dependencies

Last updated from:458a8c8ad8. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK131
source / vignettesOK200
linux-release-x86_64OK139
macos-release-arm64OK79
macos-oldrel-arm64OK76
windows-develOK93
windows-releaseOK78
windows-oldrelOK79
wasm-releaseOK129

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

Dependencies:askpassbitopsclicurldata.tablegluehttr2lifecyclemagrittropensslR6rappdirsRCurlrlangstringistringrsysvctrswithryaml

Amendments in pepr

Michal Stolarczyk

Rendered fromfeature6_amendments.Rmdusingknitr::rmarkdownon May 26 2026.

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

Getting Started with pepr

Nathan Sheffield

Rendered fromgettingStarted.Rmdusingknitr::rmarkdownon May 26 2026.

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

Sample modifiers in pepr: append

Michal Stolarczyk

Rendered fromfeature1_constantAttributes.Rmdusingknitr::rmarkdownon May 26 2026.

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

Sample modifiers in pepr: derive

Michal Stolarczyk

Rendered fromfeature3_derivedAttributes.Rmdusingknitr::rmarkdownon May 26 2026.

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

Sample modifiers in pepr: imply

Michal Stolarczyk

Rendered fromfeature2_impliedAttributes.Rmdusingknitr::rmarkdownon May 26 2026.

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

Sample modifiers in pepr: imply and derive

Michal Stolarczyk

Rendered fromfeature4_derivedImpliedAttributes.Rmdusingknitr::rmarkdownon May 26 2026.

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

Subsample table in pepr

Michal Stolarczyk & Nathan Sheffield

Rendered fromfeature5_sampleSubtable.Rmdusingknitr::rmarkdownon May 26 2026.

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

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