scGPS
This package is for version 3.10 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: 3.10
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 "3.6") 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 | 1.0.0 |
| 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, DESeq, 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_1.0.0.tar.gz |
| Windows Binary | scGPS_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | scGPS_1.0.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |