augere.core

Core Utilities for Automatically Generated Reports

Bioconductor version: 3.24 · Package version: 0.99.3

Provides utility functions for automatic generation of reports in the augere framework. This mostly involves parsing and dynamically editing Rmarkdown files, controlling inputs into the augere pipelines. Each pipeline generates and executes a self-contained Rmarkdown file for a common bioinformatics analysis; see downstream packages like augere.de and augere.screen for examples of some analysis pipelines.

DOI: 10.18129/B9.bioc.augere.core

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("augere.core")

Details

Maintainer	Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Author	Aaron Lun [cre, aut] (ORCID: <https://orcid.org/0000-0002-3564-4813>)
License	MIT + file LICENSE
URL	https://github.com/augere-bioinfo/augere.core
Bug Reports	https://github.com/augere-bioinfo/augere.core/issues
Source branch	devel
Build report	Bioconductor build system, r-universe
biocViews	ReportWriting, Software, WorkflowManagement
Package Short Url	https://bioconductor.org/packages/augere.core/

Citation

From within R, enter citation("augere.core"):

Aaron Lun. augere.core: Core Utilities for Automatically Generated Reports. doi:10.18129/B9.bioc.augere.core, R package version 0.99.3, https://bioconductor.org/packages/augere.core.

Generated from the package metadata; it may differ from the package's own citation.

Documentation

Automatic generation of analysis reports

Download

Follow the installation instructions to use this package in your R session.

Source package	augere.core_0.99.3.tar.gz
Windows binary (x86_64)	augere.core_0.99.3.zip
macOS binary (arm64)	augere.core_0.99.3.tgz
macOS binary (x86_64)	augere.core_0.99.3.tgz

Dependencies

Imports: utils, grDevices

Suggests: testthat, knitr, rmarkdown, BiocStyle, limma, edgeR, airway, S4Vectors, SummarizedExperiment, jsonlite, alabaster.base

Reverse dependencies

Imports Me (4): augere.de, augere.gsea, augere.screen, augere.solo