scGPS
This is thereleased version of scGPS; for the devel version, seescGPS.
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
Bioconductor version: Release (3.22)
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("scGPS")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("scGPS")For older versions of R, please refer to the appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 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
FollowInstallation instructions to use this package in your R session.
| Source Package | scGPS_1.24.0.tar.gz |
| Windows Binary (x86_64) | scGPS_1.24.0.zip |
| macOS Binary (x86_64) | scGPS_1.24.0.tgz |
| macOS Binary (arm64) | scGPS_1.24.0.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 |