scClassify

DOI: 10.18129/B9.bioc.scClassify    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see scClassify.

scClassify: single-cell Hierarchical Classification

Bioconductor version: 3.13

scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.

Author: Yingxin Lin

Maintainer: Yingxin Lin <yingxin.lin at sydney.edu.au>

Installation

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

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

BiocManager::install("scClassify")

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("scClassify")

 

HTML	R Script	pretrainedModel
HTML	R Script	scClassify
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, GeneExpression, SingleCell, Software
Version	1.4.0
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, pkgdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/SydneyBioX/scClassify/issues
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	scClassify_1.4.0.tar.gz
Windows Binary	scClassify_1.4.0.zip
macOS 10.13 (High Sierra)	scClassify_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scClassify
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scClassify
Package Short Url	https://bioconductor.org/packages/scClassify/
Package Downloads Report	Download Stats