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:Almut Lütge [aut, cre]

CellMixS_1.23.0.tar.gz
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CellMixS_1.23.0.tgz(r-4.4-any)CellMixS_1.23.0.tgz(r-4.3-any)
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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-1.23.0(bioc 3.21)CellMixS-1.22.0(bioc 3.20)

singlecelltranscriptomicsgeneexpressionbatcheffect

6.35 score 7 stars 64 scripts 236 downloads 1 mentions 14 exports 106 dependencies

Last updated 4 months agofrom:0d878da951. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winNOTEJan 28 2025
R-4.5-linuxNOTEJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winNOTEJan 28 2025
R-4.3-macNOTEJan 28 2025

Exports:cmsentropyevalIntegrationisildfDiffldfScelocStructuremixMetricvisClustervisGroupvisHistvisIntegrationvisMetricvisOverview

Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairoclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArraydplyrdqrngfansifarverFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelggridgesgluegridExtragtablehttrIRangesirlbaisobandjsonlitekSampleslabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngpurrrR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleSingleCellExperimentsitmosnowSparseArraystringistringrSummarizedExperimentSuppDistssyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVector

Explore data integration and batch effects

Almut Luetge, Mark D Robinson

Rendered fromCellMixS.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2019-10-23
Started: 2019-03-29

Readme and manuals

Help Manual

Help pageTopics
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
cmscms
entropyentropy
evalIntegrationevalIntegration
isiisi
ldfDiffldfDiff
ldfSceldfSce
locStructurelocStructure
mixMetricmixMetric
visClustervisCluster
visGroupvisGroup
visHistvisHist
visIntegrationvisIntegration
visMetricvisMetric
visOverviewvisOverview