OAtools

Analysis of OpenArray PCR Data

Bioconductor version: 3.23 · Package version: 1.0.0

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.

Installation

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

BiocManager::install("OAtools")

Details

Maintainer	Aidan Shea <aidantshea@gmail.com>
Author	Aidan Shea [aut, cre] (ORCID: <https://orcid.org/0009-0001-9256-7439>)
License	GPL (>= 3)
URL	https://github.com/uwvirology-ngs/OAtools
Bug Reports	https://github.com/uwvirology-ngs/OAtools/issues
Downloads rank	54
Source branch	RELEASE_3_23
biocViews	DataImport, GeneExpression, Regression, Software, qPCR

Documentation

Analyzing OpenArray Gene Expression Data with OAtools

Download

Source package

Dependencies

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)

Suggests: testthat (>= 3.0.0), knitr, kableExtra (>= 1.4.0), NormqPCR (>= 1.56.0), BiocManager (>= 1.30.27)