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 (3.23)
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("scReClassify")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, SingleCell, Software, SupportVectorMachine, Transcriptomics |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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 |
| 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | scReClassify_1.18.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | scReClassify_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | scReClassify_1.18.0.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 |