DOI: 10.18129/B9.bioc.CiteFuse  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CiteFuse.

CiteFuse: multi-modal analysis of CITE-seq data

Bioconductor version: 3.16

CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

Author: Yingxin Lin [aut, cre], Hani Kim [aut]

Maintainer: Yingxin Lin <yingxin.lin at>

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


To install this package, start R (version "4.2") 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 CiteFuse
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, SingleCell, Software
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.0)
Imports SingleCellExperiment(>= 1.8.0), SummarizedExperiment(>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, propr, uwot, Rtsne, S4Vectors(>= 0.24.0), igraph, scales, scran(>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang
Suggests knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown
Depends On Me
Imports Me
Suggests Me MuData
Links To Me
Build Report  

Package Archives

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

Source Package CiteFuse_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) CiteFuse_1.10.0.tgz
macOS Binary (arm64) CiteFuse_1.10.0.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: