DOI: 10.18129/B9.bioc.scGPS    

This is the development version of scGPS; for the stable release version, see scGPS.

A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Bioconductor version: Development (3.15)

The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.

Author: Quan Nguyen [aut, cre], Michael Thompson [aut], Anne Senabouth [aut]

Maintainer: Quan Nguyen <quan.nguyen at>

Citation (from within R, enter citation("scGPS")):


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biocViews Clustering, Coverage, DataImport, Sequencing, SingleCell, Software
Version 1.9.0
In Bioconductor since BioC 3.10 (R-3.6) (2 years)
License GPL-3
Depends R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment
Imports glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit
LinkingTo Rcpp, RcppArmadillo, RcppParallel
Suggests Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot,, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE
SystemRequirements GNU make
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Source Package scGPS_1.9.0.tar.gz
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