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

SC.MEB_1.1.tar.gz
SC.MEB_1.1.zip(r-4.5)SC.MEB_1.1.zip(r-4.4)SC.MEB_1.1.zip(r-4.3)
SC.MEB_1.1.tgz(r-4.4-x86_64)SC.MEB_1.1.tgz(r-4.4-arm64)SC.MEB_1.1.tgz(r-4.3-x86_64)SC.MEB_1.1.tgz(r-4.3-arm64)
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://shufeyangyi2015310117.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

PC - Simulated PCs
sce - A simulated SingleCellExperiment

On CRAN:

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 161 downloads 9 exports 108 dependencies

Last updated 3 years agofrom:645be6628d. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 21 2024
R-4.5-win-x86_64	NOTE	Oct 21 2024
R-4.5-linux-x86_64	NOTE	Oct 21 2024
R-4.4-win-x86_64	NOTE	Oct 21 2024
R-4.4-mac-x86_64	NOTE	Oct 21 2024
R-4.4-mac-aarch64	NOTE	Oct 21 2024
R-4.3-win-x86_64	NOTE	Oct 21 2024
R-4.3-mac-x86_64	NOTE	Oct 21 2024
R-4.3-mac-aarch64	NOTE	Oct 21 2024

Exports:ClusterPlot find_neighbors2 getneighborhood_fast ICMEM parafun SC.MEB selectK selectKPlot spatialPreprocess

Dependencies:abind askpass assorthead beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster Cairo cli cluster codetools colorspace cpp11 crayon curl DelayedArray dqrng edgeR fansi farver FNN formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 ggrastr ggrepel glue gridExtra gtable httr igraph IRanges irlba isoband jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust metapod mgcv mime munsell nlme openssl pheatmap pillar pkgconfig png purrr R6 ragg RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress rlang RSpectra rsvd Rtsne S4Arrays S4Vectors ScaledMatrix scales scater scran scuttle SingleCellExperiment sitmo snow SparseArray statmod SummarizedExperiment sys systemfonts textshaping tibble UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr XVector zlibbioc

SC-MEB

Rendered fromSC-MEB.Rmdusingknitr::rmarkdownon Oct 21 2024.

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

SC-MEB CRC

Rendered fromSC-MEB_CRC.Rmdusingknitr::rmarkdownon Oct 21 2024.

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

Citation

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