Introduction | Installation | Getting started | Load example data | Visualize batch effect | Quantify batch effects | Cellspecific Mixing scores | Parameter | Defining neighbourhoods | Further cms parameter settings | Visualize the cell mixing score | Evaluate data integration | Mixing after data integration | Compare data integration methods | Remaining batch-specific structure - ldfDiff | Visualize ldfDiff | Testing different metrics | Session info | References
Package: CellMixS 1.29.0
Almut Lütge
CellMixS: Evaluate Cellspecific Mixing
CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level.
Authors:
CellMixS_1.29.0.tar.gz
CellMixS_1.29.0.zip(r-4.7)CellMixS_1.29.0.zip(r-4.6)CellMixS_1.29.0.zip(r-4.5)
CellMixS_1.29.0.tgz(r-4.6-any)CellMixS_1.29.0.tgz(r-4.5-any)
CellMixS_1.29.0.tar.gz(r-4.7-any)CellMixS_1.29.0.tar.gz(r-4.6-any)
CellMixS_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CellMixS/json (API)
| # Install 'CellMixS' in R: |
| install.packages('CellMixS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/almutlue/cellmixs/issues
On BioConductor:CellMixS-1.29.0(bioc 3.24)CellMixS-1.28.0(bioc 3.23)
singlecelltranscriptomicsgeneexpressionbatcheffect
Last updated from:6646f69b26. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 203 | ||
| linux-devel-x86_64 | NOTE | 420 | ||
| source / vignettes | OK | 355 | ||
| linux-release-x86_64 | NOTE | 389 | ||
| macos-release-arm64 | NOTE | 165 | ||
| macos-oldrel-arm64 | NOTE | 165 | ||
| windows-devel | NOTE | 246 | ||
| windows-release | NOTE | 263 | ||
| windows-oldrel | NOTE | 281 | ||
| wasm-release | OK | 190 |
Exports:cmsentropyevalIntegrationisildfDiffldfScelocStructuremixMetricvisClustervisGroupvisHistvisIntegrationvisMetricvisOverview
Dependencies:abindassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularclicodetoolscowplotcpp11DelayedArraydplyrdqrngfarverFNNformatRfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrepelggridgesgluegridExtragtableIRangesirlbaisobandkSampleslabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspheatmappillarpkgconfigpurrrR6RColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraystringistringrSummarizedExperimentSuppDiststibbletidyrtidyselectutf8uwotvctrsviporviridisviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Toolbox to explore batch effects and data integration in scRNA data. | CellMixS-package |
| .cmsCell | .cmsCell |
| .defineSubspace | .defineSubspace |
| .filterKnn | .filterKnn |
| .filterLocMin | .filterLocMin |
| .ldfKnn | .ldfKnn |
| .smoothCms | .smoothCms |
| cms | cms |
| entropy | entropy |
| evalIntegration | evalIntegration |
| isi | isi |
| ldfDiff | ldfDiff |
| ldfSce | ldfSce |
| locStructure | locStructure |
| mixMetric | mixMetric |
| visCluster | visCluster |
| visGroup | visGroup |
| visHist | visHist |
| visIntegration | visIntegration |
| visMetric | visMetric |
| visOverview | visOverview |
