Package: SC.MEB 1.1
SC.MEB: Spatial Clustering with Hidden Markov Random Field using Empirical Bayes
Spatial clustering with hidden markov random field fitted via EM algorithm, details of which can be found in Yi Yang (2021) <doi:10.1101/2021.06.05.447181>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Authors:
SC.MEB_1.1.tar.gz
SC.MEB_1.1.tar.gz(r-4.5-noble)SC.MEB_1.1.tar.gz(r-4.4-noble)
SC.MEB_1.1.tgz(r-4.4-emscripten)SC.MEB_1.1.tgz(r-4.3-emscripten)
SC.MEB.pdf |SC.MEB.html✨
SC.MEB/json (API)
# Install 'SC.MEB' in R: |
install.packages('SC.MEB', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:645be6628d. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 31 2024 |
R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
Exports:ClusterPlotfind_neighbors2getneighborhood_fastICMEMparafunSC.MEBselectKselectKPlotspatialPreprocess
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterCairocliclustercodetoolscolorspacecpp11crayoncurlDelayedArraydqrngedgeRfansifarverFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmetapodmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngpurrrR6raggRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscranscuttleSingleCellExperimentsitmosnowSparseArraystatmodSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
ClusterPlot. | ClusterPlot |
find_neighbors2. | find_neighbors2 |
getneighborhood_fast | getneighborhood_fast |
ICMEM. | ICMEM |
parafun. | parafun |
simulated PCs | PC |
SC.MEB. | SC.MEB |
A simulated SingleCellExperiment | sce |
selectK. | selectK |
selectKPlot. | selectKPlot |
Preprocess a spatial dataset for SC-MEB | spatialPreprocess |