scReClassify
scReClassify: post hoc cell type classification of single-cell RNA-seq data
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scReClassify")Details
| Maintainer | Taiyun Kim <taiyun.kim91@gmail.com> |
| Author | Pengyi Yang [aut] (ORCID: <https://orcid.org/0000-0003-1098-3138>), Taiyun Kim [aut, cre] (ORCID: <https://orcid.org/0000-0002-5028-836X>) |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/SydneyBioX/scReClassify, http://www.bioconductor.org/packages/release/bioc/html/scReClassify.html |
| Bug Reports | https://github.com/SydneyBioX/scReClassify/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, SingleCell, Software, SupportVectorMachine, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/scReClassify/ |
Citation
From within R, enter citation("scReClassify"):
Pengyi Yang, Taiyun Kim. scReClassify: scReClassify: post hoc cell type classification of single-cell RNA-seq data. doi:10.18129/B9.bioc.scReClassify, R package version 1.18.0, https://bioconductor.org/packages/scReClassify.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | scReClassify_1.18.0.tar.gz |
| Windows binary (x86_64) | scReClassify_1.18.0.zip |
| macOS binary (arm64) | scReClassify_1.18.0.tgz |
| macOS binary (x86_64) | scReClassify_1.18.0.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods
Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr