Package: scHOT 1.17.0

Shila Ghazanfar

scHOT: single-cell higher order testing

Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.

Authors:Shila Ghazanfar [aut, cre], Yingxin Lin [aut]

scHOT_1.17.0.tar.gz
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scHOT.pdf |scHOT.html✨
scHOT/json (API)

Peer review:

On BioConductor:scHOT-1.17.0(bioc 3.20)scHOT-1.16.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

30 exports 0.71 score 73 dependencies

Last updated 2 months agofrom:e762c77628

Exports:params<-plotColouredExpressionplotEgoNetworkplotHigherOrderSequenceplotOrderedExpressionpositionColData<-positionType<-scHOTscHOT_addTestingScaffoldscHOT_buildFromMatrixscHOT_buildFromSCEscHOT_calculateGlobalHigherOrderFunctionscHOT_calculateHigherOrderTestStatisticsscHOT_estimatePvaluesscHOT_output<-scHOT_performPermutationTestscHOT_plotPermutationDistributionsscHOT_setPermutationScaffoldscHOT_setWeightMatrixscHOT_stripOutputspatialWeightMatrixtestingScaffold<-thintrajectoryWeightMatrixweightedPearsonweightedSpearmanweightedVarianceweightedZIKendallweightedZISpearmanweightMatrix<-

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurlDelayedArrayfansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2gluegtablehttrigraphIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpolyclipR6RColorBrewerRcppRcppEigenreshaperlangS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySummarizedExperimentsyssystemfontstibbletidyselecttweenrUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc