scGPS

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

Bioconductor version: 3.23 · Package version: 1.26.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scGPS")

Details

Maintainer	Quan Nguyen <quan.nguyen@uq.edu.au>
Author	Quan Nguyen [aut, cre], Michael Thompson [aut], Anne Senabouth [aut]
License	GPL-3
Bug Reports	https://github.com/IMB-Computational-Genomics-Lab/scGPS/issues
System Requirements	GNU make
Downloads rank	313
Source branch	RELEASE_3_23
biocViews	Clustering, Coverage, DataImport, Sequencing, SingleCell, Software

Documentation

scGPS introduction

Download

Source package

Dependencies

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, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE