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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 (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Clustering, Coverage, DataImport, Sequencing, SingleCell, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements GNU make
URL
Bug Reports https://github.com/IMB-Computational-Genomics-Lab/scGPS/issues
See More
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
Linking To Rcpp, RcppArmadillo, RcppParallel
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scGPS_1.17.0.tar.gz
Windows Binary scGPS_1.17.0.zip
macOS Binary (x86_64) scGPS_1.17.0.tgz
macOS Binary (arm64) scGPS_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scGPS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scGPS
Bioc Package Browser https://code.bioconductor.org/browse/scGPS/
Package Short Url https://bioconductor.org/packages/scGPS/
Package Downloads Report Download Stats