scClassify

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scClassify.

scClassify: single-cell Hierarchical Classification

Bioconductor version: 3.12

scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.

Author: Yingxin Lin

Maintainer: Yingxin Lin <yingxin.lin at sydney.edu.au>

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

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("scClassify")

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("scClassify")

pretrainedModel HTML R Script

scClassify HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, GeneExpression, SingleCell, Software

Version 1.2.0

In Bioconductor since BioC 3.11 (R-4.0) (4 years)

License GPL-3

Depends R (>= 4.0)

Imports S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod

System Requirements

URL

Bug Reports https://github.com/SydneyBioX/scClassify/issues

Suggests knitr, rmarkdown, BiocStyle, pkgdown

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