Package: OAtools 1.1.0

Aidan Shea

OAtools: Analysis of OpenArray PCR Data

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.

Authors:Aidan Shea [aut, cre]

OAtools_1.1.0.tar.gz
OAtools_1.1.0.zip(r-4.7)OAtools_1.1.0.zip(r-4.6)OAtools_1.1.0.zip(r-4.5)
OAtools_1.1.0.tgz(r-4.6-any)OAtools_1.1.0.tgz(r-4.5-any)
OAtools_1.1.0.tar.gz(r-4.7-any)OAtools_1.1.0.tar.gz(r-4.6-any)
OAtools_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
OAtools/json (API)

# Install 'OAtools' in R:

install.packages('OAtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uwvirology-ngs/oatools/issues

Datasets:

example_se - Example OpenArray Gene Expression Data Contained in a SummarizedExperiment

On BioConductor:OAtools-1.1.0(bioc 3.24)OAtools-1.0.0(bioc 3.23)

qpcr geneexpression dataimport regression

5.04 score 3 scripts 80 downloads 10 exports 107 dependencies

Last updated from:725e42103a. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	177
linux-devel-x86_64	NOTE	1189
source / vignettes	OK	1042
linux-release-x86_64	NOTE	1222
macos-release-arm64	NOTE	580
macos-oldrel-arm64	NOTE	681
windows-devel	NOTE	316
windows-release	NOTE	369
windows-oldrel	NOTE	307
wasm-release	OK	150

Exports:buildApp computeModels determinePCRResults excelToSE generateReport plotCrt plotModel plotOverview plotQC seToQPCRBatch

Dependencies:abind askpass base64enc basilisk Biobase BiocGenerics bslib cachem cellranger cli commonmark cpp11 crayon crosstalk curl data.table DelayedArray digest dir.expiry dplyr DT evaluate farver fastmap filelock fontawesome fs generics GenomicRanges ggplot2 glue gtable here highr hms htmltools htmlwidgets httpuv httr IRanges isoband janitor jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lubridate magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly png prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppTOML ReadqPCR readxl rematch reticulate rlang rmarkdown rprojroot S4Arrays S4Vectors S7 sass scales Seqinfo shiny snakecase sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect timechange tinytex utf8 vctrs viridisLite withr writexl xfun xtable XVector yaml

Analyzing OpenArray Gene Expression Data with OAtools

Rendered fromOAtools.Rmdusingknitr::rmarkdown

Last update: 2026-01-30
Started: 2025-09-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Web Server	.buildServer
User Interface	.buildUI
Run the fit_curve() function	.runFitCurve
Data Import Server	.serverDataImport
Curve Fitting Server	.serverFitCurves
Graphics Server	.serverGraphics
Reporting Server	.serverReporting
Data Import UI	.uiDataImport
Curve Fitting UI	.uiFitCurves
Graphics UI	.uiGraphics
Reporting UI	.uiReporting
A Shiny App for OAtools	buildApp
Optimize 5PL models to OpenArray PCR data and save as metadata	computeModels
Determine PCR results from fit curves	determinePCRResults
Example OpenArray Gene Expression Data Contained in a SummarizedExperiment	example_se
Convert OpenArray data from Excel to a Summarized Experiment	excelToSE
Generate a PCR Report	generateReport
Example Raw OpenArray Gene Expression Data	oa_gene_expression_1
Example Raw OpenArray Gene Expression Data	oa_gene_expression_2
Plot Relative Cycle Threshold Values by Gene	plotCrt
Plot Fluorescence Values Predicted by Model	plotModel
Plot Amplification Status by Sample and Gene	plotOverview
Plot a 3D Quality Control Graphic from a SummarizedExperiment	plotQC
Convert to qPCRBatch Object	seToQPCRBatch
Target Threshold Key	target_threshold_key