scGPS

This package is for version 3.19 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: 3.19

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, Coverage, DataImport, Sequencing, SingleCell, Software

Version 1.18.0

In Bioconductor since BioC 3.10 (R-3.6) (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

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

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Links To Me

Build Report Build Report

Package Archives

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

Source Package scGPS_1.18.0.tar.gz

Windows Binary (x86_64) scGPS_1.18.0.zip

macOS Binary (x86_64) scGPS_1.18.0.tgz

macOS Binary (arm64) scGPS_1.18.0.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/

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