To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("HTqPCR")
In most cases, you don't need to download the package archive at all.
HTqPCR
Automated analysis of high-throughput qPCR data
Bioconductor version: 3.0
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: Heidi Dvinge <heidi at ebi.ac.uk>
Citation (from within R,
enter citation("HTqPCR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("HTqPCR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HTqPCR")
| R Script | qPCR analysis in R | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) |
| License | Artistic-2.0 |
| Depends | Biobase, RColorBrewer, limma |
| Imports | affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils |
| LinkingTo | |
| Suggests | statmod |
| SystemRequirements | |
| Enhances | |
| URL | http://www.ebi.ac.uk/bertone/software |
| Depends On Me | |
| Imports Me | nondetects, unifiedWMWqPCR |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | HTqPCR_1.20.0.tar.gz |
| Windows Binary | HTqPCR_1.20.0.zip |
| Mac OS X 10.6 (Snow Leopard) | HTqPCR_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | HTqPCR_1.20.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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