uSORT

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see uSORT.

uSORT: A self-refining ordering pipeline for gene selection


Bioconductor version: 3.10

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 "3.6") 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 1.12.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements
URL
See More
Suggests knitr, RUnit, testthat, ggplot2
Linking To
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 uSORT_1.12.0.tar.gz
Windows Binary uSORT_1.12.0.zip
Mac OS X 10.11 (El Capitan) uSORT_1.12.0.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
Old Source Packages for BioC 3.10 Source Archive