uSORT

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see uSORT.

uSORT: A self-refining ordering pipeline for gene selection

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBiology, DNASeq, GUI, ImmunoOncology, RNASeq, Software

Version 1.20.0

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

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Suggests knitr, RUnit, testthat, ggplot2

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Build Report Build Report

Package Archives

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

Source Package uSORT_1.20.0.tar.gz

Windows Binary uSORT_1.20.0.zip

macOS 10.13 (High Sierra) uSORT_1.20.0.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 3.14 Source Archive