Package: pepr 0.5.0

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]

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pepr.pdf |pepr.html✨
pepr/json (API)
NEWS

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

Peer review:

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

On CRAN:

bioinformaticsmetadata

6.05 score 4 stars 20 scripts 245 downloads 1 mentions 19 exports 19 dependencies

Last updated 1 years agofrom:150b52dcce. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winOKNov 18 2024
R-4.5-linuxOKNov 18 2024
R-4.4-winOKNov 18 2024
R-4.4-macOKNov 18 2024
R-4.3-winOKNov 18 2024
R-4.3-macOKNov 18 2024

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

Dependencies:bitopsclicodetoolscpp11crayondata.tablegluelifecyclelobstrmagrittrprettyunitspryrRcppRCurlrlangstringistringrvctrsyaml

Amendments in pepr

Michal Stolarczyk

Rendered fromfeature6_amendments.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-11-16
Started: 2020-05-26

Getting Started with pepr

Nathan Sheffield

Rendered fromgettingStarted.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2020-10-15
Started: 2017-10-26

Sample modifiers in pepr: append

Michal Stolarczyk

Rendered fromfeature1_constantAttributes.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Sample modifiers in pepr: derive

Michal Stolarczyk

Rendered fromfeature3_derivedAttributes.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Sample modifiers in pepr: imply

Michal Stolarczyk

Rendered fromfeature2_impliedAttributes.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Sample modifiers in pepr: imply and derive

Michal Stolarczyk

Rendered fromfeature4_derivedImpliedAttributes.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Subsample table in pepr

Michal Stolarczyk & Nathan Sheffield

Rendered fromfeature5_sampleSubtable.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-11-17
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
The constructor of a class representing a Portable Encapsulated ProjectProject
Portable Encapsulated Project objectProject-class
View samples in the objects of '"Project"'sampleTable sampleTable,Project-method
Access '"Config"' object elements$,Config-method select-config [,Config-method [[,Config-method