Package: NormqPCR 1.53.0
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_1.53.0.tar.gz
NormqPCR_1.53.0.zip(r-4.5)NormqPCR_1.53.0.zip(r-4.4)NormqPCR_1.53.0.zip(r-4.3)
NormqPCR_1.53.0.tgz(r-4.4-any)NormqPCR_1.53.0.tgz(r-4.3-any)
NormqPCR_1.53.0.tar.gz(r-4.5-noble)NormqPCR_1.53.0.tar.gz(r-4.4-noble)
NormqPCR_1.53.0.tgz(r-4.4-emscripten)NormqPCR_1.53.0.tgz(r-4.3-emscripten)
NormqPCR.pdf |NormqPCR.html✨
NormqPCR/json (API)
| # Install 'NormqPCR' in R: |
| install.packages('NormqPCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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-1.53.0(bioc 3.21)NormqPCR-1.52.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microtitreplateassaygeneexpressionqpcr
Last updated 2 months agofrom:291a5b8a1d. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:combineTechRepscombineTechRepsWithSDComputeNRQsCqValuesdeltaCqdeltaCtdeltaDeltaCqdeltaDeltaCtgeomMeanmakeAllNAsmakeAllNewValreplaceAboveCutOffreplaceNAsselectHKsstabMeasureMstabMeasureRho
Dependencies:base64encBiobaseBiocGenericsbslibcachemcliDEoptimRdigestevaluatefastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlatticelifecyclemagrittrMASSMatrixmemoisemimeminpack.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 |
