Package: CellMixS 1.23.0
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_1.23.0.tar.gz
CellMixS_1.23.0.zip(r-4.5)CellMixS_1.23.0.zip(r-4.4)CellMixS_1.23.0.zip(r-4.3)
CellMixS_1.23.0.tgz(r-4.4-any)CellMixS_1.23.0.tgz(r-4.3-any)
CellMixS_1.23.0.tar.gz(r-4.5-noble)CellMixS_1.23.0.tar.gz(r-4.4-noble)
CellMixS_1.23.0.tgz(r-4.4-emscripten)CellMixS_1.23.0.tgz(r-4.3-emscripten)
CellMixS.pdf |CellMixS.html✨
CellMixS/json (API)
NEWS
| # 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-1.21.1(bioc 3.20)CellMixS-1.20.0(bioc 3.19)
singlecelltranscriptomicsgeneexpressionbatcheffect
Last updated 23 days agofrom:0d878da951. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:cmsentropyevalIntegrationisildfDiffldfScelocStructuremixMetricvisClustervisGroupvisHistvisIntegrationvisMetricvisOverview
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairoclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArraydplyrdqrngfansifarverFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelggridgesgluegridExtragtablehttrIRangesirlbaisobandjsonlitekSampleslabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngpurrrR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleSingleCellExperimentsitmosnowSparseArraystringistringrSummarizedExperimentSuppDistssyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
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 |
