DOI: 10.18129/B9.bioc.clustifyr  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see clustifyr.

Classifier for Single-cell RNA-seq Using Cell Clusters

Bioconductor version: 3.17

Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

Author: Rui Fu [aut], Kent Riemondy [cre, aut], Austin Gillen [ctb], Chengzhe Tian [ctb], Jay Hesselberth [ctb], Yue Hao [ctb], Michelle Daya [ctb], Sidhant Puntambekar [ctb], RNA Bioscience Initiative [fnd, cph]

Maintainer: Kent Riemondy <kent.riemondy at>

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


To install this package, start R (version "4.3") and enter:

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


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:



HTML R Script geo-annotations
HTML R Script Introduction to clustifyr
PDF   Reference Manual
Text   NEWS


biocViews Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software
Version 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0)
Imports cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, matrixStats, S4Vectors, proxy, httr, utils
Suggests ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr
Depends On Me
Imports Me
Suggests Me clustifyrdatahub
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package clustifyr_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64) clustifyr_1.12.0.tgz
macOS Binary (arm64) clustifyr_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: