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")):
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")
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 (>= 4.6) |
| 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), 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/OAtools/ |
| Package Short Url | https://bioconductor.org/packages/OAtools/ |
| Package Downloads Report | Download Stats |