scReClassify

DOI: 10.18129/B9.bioc.scReClassify  

scReClassify: post hoc cell type classification of single-cell RNA-seq data

Bioconductor version: Release (3.16)

A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.

Author: Pengyi Yang [aut] , Taiyun Kim [aut, cre]

Maintainer: Taiyun Kim <taiyun.kim91 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("scReClassify")

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("scReClassify")

 

HTML	R Script	An introduction to scReClassify package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, SingleCell, Software, SupportVectorMachine, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1)
Imports	randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods
LinkingTo
Suggests	testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
SystemRequirements
Enhances
URL	https://github.com/SydneyBioX/scReClassify http://www.bioconductor.org/packages/release/bioc/html/scReClassify.html
BugReports	https://github.com/SydneyBioX/scReClassify/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	scReClassify_1.4.0.tar.gz
Windows Binary	scReClassify_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	scReClassify_1.4.0.tgz
macOS Binary (arm64)	scReClassify_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scReClassify
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scReClassify
Bioc Package Browser	https://code.bioconductor.org/browse/scReClassify/
Package Short Url	https://bioconductor.org/packages/scReClassify/
Package Downloads Report	Download Stats