Package: SC.MEB 1.1

Yi Yang

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:Yi Yang [aut, cre], Xingjie Shi [aut], Jin Liu [aut]

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'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • PC - Simulated PCs
  • sce - A simulated SingleCellExperiment

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

3.00 score 10 scripts 181 downloads 9 exports 108 dependencies

Last updated 3 years agofrom:645be6628d. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 19 2024
R-4.5-linux-x86_64NOTESep 19 2024

Exports:ClusterPlotfind_neighbors2getneighborhood_fastICMEMparafunSC.MEBselectKselectKPlotspatialPreprocess

Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterCairocliclustercodetoolscolorspacecpp11crayoncurlDelayedArraydqrngedgeRfansifarverFNNformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmetapodmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngpurrrR6raggRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscranscuttleSingleCellExperimentsitmosnowSparseArraystatmodSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc

SC-MEB

Rendered fromSC-MEB.Rmdusingknitr::rmarkdownon Sep 19 2024.

Last update: 2021-10-08
Started: 2021-07-16

SC-MEB CRC

Rendered fromSC-MEB_CRC.Rmdusingknitr::rmarkdownon Sep 19 2024.

Last update: 2021-10-08
Started: 2021-10-08