OAtools
This is the development version of OAtools; to use it, please install the devel version of Bioconductor.
Analysis of OpenArray PCR Data
Bioconductor version: Development (3.23)
Provides a suite of R functions to analyze gene expression experiments on the OpenArray real-time PCR platform. OAtools fits logistic regressions to fluorescence curves to distinguish between real amplification and false positives. OAtools supports data import, analysis, and visualization through plots and a dynamic HTML report.
Maintainer: Aidan Shea <aidantshea at gmail.com>
citation("OAtools")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("OAtools")
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("OAtools")| Analyzing OpenArray Gene Expression Data with OAtools | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, GeneExpression, Regression, Software, qPCR |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.6) |
| Imports | basilisk(>= 1.20.0), Biobase(>= 2.70.0), dplyr (>= 1.1.4), DT (>= 0.34.0), ggplot2 (>= 3.5.2), janitor (>= 2.2.1), methods (>= 4.5.2), plotly (>= 4.11.0), purrr (>= 1.2.0), ReadqPCR(>= 1.56.0), readxl (>= 1.4.5), reticulate (>= 1.43.0), rlang (>= 1.1.6), rmarkdown (>= 2.29), S4Vectors(>= 0.48.0), SummarizedExperiment(>= 1.40.0), tibble (>= 3.3.0), tidyr (>= 1.3.1) |
| System Requirements | |
| URL | https://github.com/uwvirology-ngs/OAtools |
| Bug Reports | https://github.com/uwvirology-ngs/OAtools/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, kableExtra (>= 1.4.0), NormqPCR(>= 1.56.0), BiocManager (>= 1.30.27) |
| 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 | OAtools_0.99.9.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/OAtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OAtools |
| Bioc Package Browser | https://code.bioconductor.org/browse/OAtools/ |
| Package Short Url | https://bioconductor.org/packages/OAtools/ |
| Package Downloads Report | Download Stats |