augere.core
This is the development version of augere.core; to use it, please install the devel version of Bioconductor.
Core Utilities for Automatically Generated Reports
Bioconductor version: Development (3.24)
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.
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("augere.core")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("augere.core")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("augere.core")| Creating analysis pipelines | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ReportWriting, Software, WorkflowManagement |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | utils, grDevices |
| System Requirements | |
| URL | https://github.com/augere-bioinfo/augere.core |
| Bug Reports | https://github.com/augere-bioinfo/augere.core/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, limma, edgeR, airway, S4Vectors, SummarizedExperiment, jsonlite, alabaster.base |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | augere.core_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | augere.core_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/augere.core |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/augere.core |
| Bioc Package Browser | https://code.bioconductor.org/browse/augere.core/ |
| Package Short Url | https://bioconductor.org/packages/augere.core/ |
| Package Downloads Report | Download Stats |