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scGPS

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Clustering, Coverage, DataImport, Sequencing, SingleCell, Software
Version 1.14.1
In Bioconductor since BioC 3.10 (R-3.6) (4 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
Linking To 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
System Requirements GNU make
Enhances
URL
Bug Reports https://github.com/IMB-Computational-Genomics-Lab/scGPS/issues
See More
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_1.14.1.tar.gz
Windows Binary scGPS_1.14.1.zip
macOS Binary (x86_64) scGPS_1.14.1.tgz
macOS Binary (arm64) scGPS_1.14.1.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
Old Source Packages for BioC 3.17 Source Archive