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 (3.21)
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] (ORCID:
Maintainer: Taiyun Kim <taiyun.kim91 at gmail.com>
citation("scReClassify")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, SingleCell, Software, SupportVectorMachine, Transcriptomics |
| Version | 1.13.0 |
| 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 |
See More
| Suggests | testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr |
| 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 | scReClassify_1.13.0.tar.gz |
| Windows Binary (x86_64) | scReClassify_1.13.0.zip |
| macOS Binary (x86_64) | scReClassify_1.13.0.tgz |
| macOS Binary (arm64) | scReClassify_1.13.0.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 |