uSORT

DOI: 10.18129/B9.bioc.uSORT    

uSORT: A self-refining ordering pipeline for gene selection

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Quick Start
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBiology, DNASeq, GUI, ImmunoOncology, RNASeq, Software
Version	1.18.0
In Bioconductor since	BioC 3.4 (R-3.3) (5 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
LinkingTo
Suggests	knitr, RUnit, testthat, ggplot2
SystemRequirements
Enhances
URL
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	uSORT_1.18.0.tar.gz
Windows Binary	uSORT_1.18.0.zip
macOS 10.13 (High Sierra)	uSORT_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/uSORT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/uSORT
Package Short Url	https://bioconductor.org/packages/uSORT/
Package Downloads Report	Download Stats