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

scClassify: single-cell Hierarchical Classification

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

pretrainedModel HTML R Script
scClassify HTML R Script
Reference Manual PDF


biocViews Classification, GeneExpression, SingleCell, Software
Version 1.17.0
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, Cepo
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Follow Installation instructions to use this package in your R session.

Source Package scClassify_1.17.0.tar.gz
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macOS Binary (x86_64) scClassify_1.17.0.tgz
macOS Binary (arm64) scClassify_1.17.0.tgz
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