scGPS

DOI: 10.18129/B9.bioc.scGPS    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date 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: 3.13

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 uq.edu.au>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("scGPS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scGPS")

 

HTML	R Script	single cell Global fate Potential of Subpopulations
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, Coverage, DataImport, Sequencing, SingleCell, Software
Version	1.6.0
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, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE
SystemRequirements	GNU make
Enhances
URL
BugReports	https://github.com/IMB-Computational-Genomics-Lab/scGPS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scGPS_1.6.0.tar.gz
Windows Binary	scGPS_1.6.0.zip
macOS 10.13 (High Sierra)	scGPS_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scGPS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scGPS
Package Short Url	https://bioconductor.org/packages/scGPS/
Package Downloads Report	Download Stats