scReClassify

This is the released version of scReClassify; for the devel version, see scReClassify.

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

Bioconductor version: Release (3.20)

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>

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

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, SingleCell, Software, SupportVectorMachine, Transcriptomics
Version	1.12.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1)
Imports	randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods
System Requirements
URL	https://github.com/SydneyBioX/scReClassify http://www.bioconductor.org/packages/release/bioc/html/scReClassify.html
Bug Reports	https://github.com/SydneyBioX/scReClassify/issues

Suggests	testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
Linking To
Enhances
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Build Report	Build Report

Package Archives

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

Source Package	scReClassify_1.12.0.tar.gz
Windows Binary (x86_64)	scReClassify_1.12.0.zip
macOS Binary (x86_64)	scReClassify_1.12.0.tgz
macOS Binary (arm64)	scReClassify_1.12.0.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

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