HTqPCR
This is the development version of HTqPCR; for the stable release version, see HTqPCR.
Automated analysis of high-throughput qPCR data
Bioconductor version: Development (3.24)
Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).
Author: Heidi Dvinge, Paul Bertone
Maintainer: Matthew N. McCall <mccallm at gmail.com>
citation("HTqPCR")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("HTqPCR")
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("HTqPCR")| qPCR analysis in R | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR |
| Version | 1.67.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | Artistic-2.0 |
| Depends | Biobase, RColorBrewer, limma |
| Imports | affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils |
| System Requirements | |
| URL | http://www.ebi.ac.uk/bertone/software |
See More
| Suggests | statmod |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | nondetects |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HTqPCR_1.67.0.tar.gz |
| Windows Binary (x86_64) | HTqPCR_1.67.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HTqPCR_1.67.0.tgz |
| macOS Binary (sonoma-arm64) | HTqPCR_1.67.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HTqPCR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HTqPCR |
| Bioc Package Browser | https://code.bioconductor.org/browse/HTqPCR/ |
| Package Short Url | https://bioconductor.org/packages/HTqPCR/ |
| Package Downloads Report | Download Stats |