DOI: 10.18129/B9.bioc.clustifyr    

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

Classifier for Single-cell RNA-seq Using Cell Clusters

Bioconductor version: Development (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")):


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biocViews Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software
Version 1.11.0
In Bioconductor since BioC 3.11 (R-4.0) (2.5 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
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