augere.de
This is the development version of augere.de; to use it, please install the devel version of Bioconductor.
Automatic Generation of Differential Expression Analyses
Bioconductor version: Development (3.24)
Implements pipelines for generating differential expression analysis reports in the augere framework. This includes analyses with edgeR or voom-limma, with a variety of options for contrasts, blocking and covariates. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce the DE analysis.
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("augere.de")):
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.de")
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.de")| Differential expression analyses | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, ReportWriting, Software, Transcription, WorkflowManagement |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | utils, methods, limma, edgeR, S4Vectors, augere.core, alabaster.se |
| System Requirements | |
| URL | https://github.com/augere-bioinfo/augere.de |
| Bug Reports | https://github.com/augere-bioinfo/augere.de/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, airway, SummarizedExperiment |
| 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.de_0.99.2.tar.gz |
| Windows Binary (x86_64) | augere.de_0.99.2.zip |
| macOS Binary (big-sur-x86_64) | augere.de_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | augere.de_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/augere.de |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/augere.de |
| Bioc Package Browser | https://code.bioconductor.org/browse/augere.de/ |
| Package Short Url | https://bioconductor.org/packages/augere.de/ |
| Package Downloads Report | Download Stats |