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scClassify

This is the development version of scClassify; for the stable release version, see scClassify.

scClassify: single-cell Hierarchical Classification


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL
Bug Reports https://github.com/SydneyBioX/scClassify/issues
See More
Suggests knitr, rmarkdown, BiocStyle, pkgdown
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 scClassify_1.15.0.tar.gz
Windows Binary scClassify_1.15.0.zip (64-bit only)
macOS Binary (x86_64) scClassify_1.15.0.tgz
macOS Binary (arm64) scClassify_1.15.0.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