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scClassify

scClassify: single-cell Hierarchical Classification

Bioconductor version: Release (3.17)

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>

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

Installation

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

if (!require("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")
pretrainedModel HTML R Script
scClassify HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, GeneExpression, SingleCell, Software
Version 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 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, Cepo
Linking To
Suggests knitr, rmarkdown, BiocStyle, pkgdown
System Requirements
Enhances
URL
Bug Reports https://github.com/SydneyBioX/scClassify/issues
See More
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_1.12.0.tar.gz
Windows Binary scClassify_1.12.0.zip
macOS Binary (x86_64) scClassify_1.12.0.tgz
macOS Binary (arm64) scClassify_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scClassify
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scClassify
Bioc Package Browser https://code.bioconductor.org/browse/scClassify/
Package Short Url https://bioconductor.org/packages/scClassify/
Package Downloads Report Download Stats