1 Introduction | 2 Run SCnorm | 3 SCnorm: Multiple Conditions | 4 SCnorm: UMI data | 5 Spike-ins | 6 Within-sample normalization | 7 Session info | 8 Frequently Asked Questions
Package: SCnorm 1.35.0
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_1.35.0.tar.gz
SCnorm_1.35.0.zip(r-4.7)SCnorm_1.35.0.zip(r-4.6)SCnorm_1.35.0.zip(r-4.5)
SCnorm_1.35.0.tgz(r-4.6-any)SCnorm_1.35.0.tgz(r-4.5-any)
SCnorm_1.35.0.tar.gz(r-4.7-any)SCnorm_1.35.0.tar.gz(r-4.6-any)
SCnorm_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SCnorm/json (API)
| # 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
Datasets:
- ExampleSimSCData - Example datasets for SCnorm
On BioConductor:SCnorm-1.35.0(bioc 3.24)SCnorm-1.34.0(bioc 3.23)
normalizationrnaseqsinglecellimmunooncology
Last updated from:3ceb26a3ad. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 208 | ||
| linux-devel-x86_64 | NOTE | 309 | ||
| source / vignettes | OK | 470 | ||
| linux-release-x86_64 | NOTE | 345 | ||
| macos-release-arm64 | NOTE | 149 | ||
| macos-oldrel-arm64 | NOTE | 148 | ||
| windows-devel | NOTE | 229 | ||
| windows-release | NOTE | 237 | ||
| windows-oldrel | NOTE | 248 | ||
| wasm-release | OK | 184 |
Exports:getCountsgetSlopesplotCountDepthplotWithinFactorresultsscaleNormMultContSCnorm
Dependencies:abindBHBiobaseBiocGenericsBiocParallelcliclustercodetoolscpp11data.tableDelayedArrayfarverforcatsformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmomentspillarpkgconfigquantregR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraySparseMSummarizedExperimentsurvivaltibbleutf8vctrsviridisLitewithrXVector
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 |
