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 (3.19)
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 | ||
NEWS | Text |
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 |
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_1.18.0.tar.gz |
Windows Binary | 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/ |
Package Downloads Report | Download Stats |