Package: SCnorm 1.27.0
Rhonda Bacher
SCnorm: Normalization of single cell RNA-seq data
This package implements SCnorm — a method to normalize single-cell RNA-seq data.
Authors:
SCnorm_1.27.0.tar.gz
SCnorm_1.27.0.zip(r-4.5)SCnorm_1.27.0.zip(r-4.4)SCnorm_1.27.0.zip(r-4.3)
SCnorm_1.27.0.tgz(r-4.4-any)SCnorm_1.27.0.tgz(r-4.3-any)
SCnorm_1.27.0.tar.gz(r-4.5-noble)SCnorm_1.27.0.tar.gz(r-4.4-noble)
SCnorm_1.27.0.tgz(r-4.4-emscripten)SCnorm_1.27.0.tgz(r-4.3-emscripten)
SCnorm.pdf |SCnorm.html✨
SCnorm/json (API)
NEWS
| # Install 'SCnorm' in R: |
| install.packages('SCnorm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rhondabacher/scnorm/issues
- ExampleSimSCData - Example datasets for SCnorm
On BioConductor:SCnorm-1.27.0(bioc 3.20)SCnorm-1.26.0(bioc 3.19)
Last updated 2 months agofrom:c1148767dd
Exports:getCountsgetSlopesplotCountDepthplotWithinFactorresultsscaleNormMultContSCnorm
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayfansifarverforcatsformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmimemomentsmunsellnlmeopensslpillarpkgconfigquantregR6RColorBrewerrlangS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySparseMSummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| correctWithin | correctWithin |
| Evaluate normalization using K slope groups | evaluateK |
| Example datasets for SCnorm | ExampleSimSCData |
| Internal plotting function. | generateEvalPlot |
| getCounts | getCounts |
| getDens | getDens |
| Estimate gene specific count-depth relationships | getSlopes |
| Fit group regression for specific quantile and degree | GetTD |
| Iteratively fit group regression and evaluate to choose optimal K | normWrapper |
| Evaluate the count-depth relationship before (or after) normalizing the data. | plotCountDepth |
| Evaluate gene-specific factors in the the data. | plotWithinFactor |
| quickReg | quickReg |
| redoBox | redoBox |
| results | results |
| Scale multiple conditions | scaleNormMultCont |
| SCnorm | SCnorm |
| Fit group quantile regression for K groups | SCnormFit |
| splitGroups | splitGroups |
