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uSORT

uSORT: A self-refining ordering pipeline for gene selection

Bioconductor version: Release (3.17)

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.

Author: Mai Chan Lau, Hao Chen, Jinmiao Chen

Maintainer: Hao Chen <chen_hao at immunol.a-star.edu.sg>

Citation (from within R, enter citation("uSORT")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("uSORT")

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("uSORT")
Quick Start HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBiology, DNASeq, GUI, ImmunoOncology, RNASeq, Software
Version 1.26.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License Artistic-2.0
Depends R (>= 3.3.0), tcltk
Imports igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils
Linking To
Suggests knitr, RUnit, testthat, ggplot2
System Requirements
Enhances
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Build Report  

Package Archives

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

Source Package uSORT_1.26.0.tar.gz
Windows Binary uSORT_1.26.0.zip
macOS Binary (x86_64) uSORT_1.26.0.tgz
macOS Binary (arm64) uSORT_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/uSORT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/uSORT
Bioc Package Browser https://code.bioconductor.org/browse/uSORT/
Package Short Url https://bioconductor.org/packages/uSORT/
Package Downloads Report Download Stats