Package: miloR 2.1.0
miloR: Differential neighbourhood abundance testing on a graph
Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either a negative bionomial generalized linear model or negative binomial generalized linear mixed model.
Authors:
miloR_2.1.0.tar.gz
miloR_2.1.0.zip(r-4.5)miloR_2.1.0.zip(r-4.4)miloR_2.1.0.zip(r-4.3)
miloR_2.1.0.tgz(r-4.4-arm64)miloR_2.1.0.tgz(r-4.4-x86_64)miloR_2.1.0.tgz(r-4.3-arm64)miloR_2.1.0.tgz(r-4.3-x86_64)
miloR_2.1.0.tar.gz(r-4.5-noble)miloR_2.1.0.tar.gz(r-4.4-noble)
miloR_2.1.0.tgz(r-4.4-emscripten)miloR_2.1.0.tgz(r-4.3-emscripten)
miloR.pdf |miloR.html✨
miloR/json (API)
NEWS
# Install 'miloR' in R: |
install.packages('miloR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/marionilab/milor/issues
- sim_discrete - Sim_discrete
- sim_family - Sim_family
- sim_nbglmm - Sim_nbglmm
- sim_trajectory - Simulated linear trajectory data
On BioConductor:miloR-2.1.0(bioc 3.20)miloR-2.0.0(bioc 3.19)
Last updated 2 months agofrom:15c14c9743
Exports:.calc_distance.parse_formula.rEParseannotateNhoodsbuildFromAdjacencybuildGraphbuildNhoodGraphcalcNhoodDistancecalcNhoodExpressioncheckSeparationcomputePvaluecountCellsfindNhoodGroupMarkersfindNhoodMarkersfitGLMMglmmControl.defaultsgraphgraph<-graphSpatialFDRgroupNhoodsinitialiseGinitializeFullZmakeNhoodsmatrix.traceMilonhoodAdjacencynhoodAdjacency<-nhoodCountsnhoodCounts<-nhoodDistancesnhoodDistances<-nhoodExpressionnhoodExpression<-nhoodGraphnhoodGraph<-nhoodIndexnhoodIndex<-nhoodReducedDimnhoodReducedDim<-nhoodsnhoods<-plotDAbeeswarmplotNhoodCountsplotNhoodExpressionDAplotNhoodExpressionGroupsplotNhoodGraphplotNhoodGraphDAplotNhoodGroupsplotNhoodMAplotNhoodSizeHistSatterthwaite_dfshowtestDiffExptestNhoods
Dependencies:abindaskpassbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularcachemclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArraydplyredgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtablegtoolshttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmenumDerivopensslpatchworkpillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenRcppHNSWrlangrsvdS4ArraysS4VectorsScaledMatrixscalesSingleCellExperimentsnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttweenrUCSC.utilsutf8vctrsviporviridisviridisLitewithrXVectorzlibbioc