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scReClassify

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

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


Bioconductor version: Development (3.19)

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")

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

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

Details

biocViews Classification, SingleCell, Software, SupportVectorMachine, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
See More
Suggests testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
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Build Report Build Report

Package Archives

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

Source Package scReClassify_1.9.0.tar.gz
Windows Binary scReClassify_1.9.0.zip
macOS Binary (x86_64) scReClassify_1.9.0.tgz
macOS Binary (arm64) scReClassify_1.9.0.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