OAtools
This is the released version of OAtools; for the devel version, see OAtools.
Analysis of OpenArray PCR Data
Bioconductor version: Release (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")):Aidan Shea. OAtools: Analysis of OpenArray PCR Data. doi:10.18129/B9.bioc.OAtools, R package version 1.0.0, https://bioconductor.org/packages/OAtools.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5) |
| 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), shiny (>= 1.13.0), SummarizedExperiment (>= 1.40.0), tibble (>= 3.3.0), tidyr (>= 1.3.1), writexl (>= 1.5.4) |
| 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | OAtools_1.0.0.tar.gz |
| Windows Binary (x86_64) | OAtools_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | OAtools_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | OAtools_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/OAtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OAtools |
| Package Short Url | https://bioconductor.org/packages/OAtools/ |
| Package Downloads Report | Download Stats |