Introduction | Combining technical replicates | Dealing with undetermined values | Selection of most stable reference/housekeeping genes | Normalization by means of reference/housekeeping genes
Package: NormqPCR 1.59.0
James Perkins
NormqPCR: Functions for normalisation of RT-qPCR data
Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.
Authors:
NormqPCR_1.59.0.tar.gz
NormqPCR_1.59.0.zip(r-4.7)NormqPCR_1.59.0.zip(r-4.6)NormqPCR_1.59.0.zip(r-4.5)
NormqPCR_1.59.0.tgz(r-4.6-any)NormqPCR_1.59.0.tgz(r-4.5-any)
NormqPCR_1.59.0.tar.gz(r-4.7-any)NormqPCR_1.59.0.tar.gz(r-4.6-any)
NormqPCR_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
NormqPCR/json (API)
| # Install 'NormqPCR' in R: |
| install.packages('NormqPCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- Bladder - Bladder dataset of Andersen et al
- BladderRepro - Dataset of Andersen et al
- Colon - Colon dataset of Andersen et al
- geNorm.qPCRBatch - Data set of Vandesompele et al
On BioConductor:NormqPCR-1.59.0(bioc 3.24)NormqPCR-1.58.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microtitreplateassaygeneexpressionqpcr
Last updated from:f67ff4e43b. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 187 | ||
| linux-devel-x86_64 | NOTE | 223 | ||
| source / vignettes | OK | 202 | ||
| linux-release-x86_64 | NOTE | 213 | ||
| macos-release-arm64 | NOTE | 109 | ||
| macos-oldrel-arm64 | NOTE | 91 | ||
| windows-devel | NOTE | 171 | ||
| windows-release | NOTE | 140 | ||
| windows-oldrel | NOTE | 150 | ||
| wasm-release | OK | 142 |
Exports:combineTechRepscombineTechRepsWithSDComputeNRQsCqValuesdeltaCqdeltaCtdeltaDeltaCqdeltaDeltaCtgeomMeanmakeAllNAsmakeAllNewValreplaceAboveCutOffreplaceNAsselectHKsstabMeasureMstabMeasureRho
Dependencies:base64encBiobaseBiocGenericsbslibcachemcliDEoptimRdigestevaluatefastmapfontawesomefsgenericshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlatticelifecyclemagrittrMASSMatrixmemoisemimeminpack.lmqpcRR6rappdirsRColorBrewerReadqPCRrglrlangrmarkdownrobustbasesasstinytexxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Functions for normalisation of RT-qPCR data. | NormqPCR-package NormqPCR |
| Bladder dataset of Andersen et al (2004) | Bladder |
| Dataset of Andersen et al (2004) | BladderRepro BladderRepro.qPCRBatch |
| Colon dataset of Andersen et al (2004) | Colon |
| Combines Technical Replicates | combineTechReps combineTechReps,qPCRBatch-method |
| Combines Technical Replicates | combineTechRepsWithSD combineTechRepsWithSD,qPCRBatch-method |
| Compute Normalized Relative Quantities | ComputeNRQs ComputeNRQs,qPCRBatch-method ComputeNRQs-methods |
| Compute Cq value and amplification efficiency | CqValues CqValues,CyclesSet-method CqValues-methods |
| Perform normalization with a given housekeeping gene | deltaCq deltaCt deltaCt,qPCRBatch-method deltaCt-methods |
| Perform normalization and differential expression with given housekeeping gene | deltaDeltaCq deltaDeltaCq,qPCRBatch-method deltaDeltaCq-methods deltaDeltaCt deltaDeltaCt,qPCRBatch-method deltaDeltaCt-methods |
| Data set of Vandesompele et al (2002) | geNorm geNorm.qPCRBatch |
| Geometric Mean | geomMean |
| Make all Cq values NA | makeAllNAs makeAllNAs,qPCRBatch-method |
| Make all Cq values NA | makeAllNewVal makeAllNewVal,qPCRBatch-method |
| Replace Cq values with new value | replaceAboveCutOff replaceAboveCutOff,qPCRBatch-method |
| Replace NAs with a given value | replaceNAs replaceNAs,qPCRBatch-method |
| Selection of reference/housekeeping genes | selectHKs selectHKs,matrix-method selectHKs,qPCRBatch-method selectHKs-methods |
| Gene expression stability value M | stabMeasureM |
| Gene expression stability value rho | stabMeasureRho stabMeasureRho,matrix-method stabMeasureRho,qPCRBatch-method stabMeasureRho,x-method stabMeasureRho-methods |
