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CiteFuse: multi-modal analysis of CITE-seq data

Bioconductor version: Release (3.19)

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 "4.4") 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:

CiteFuse HTML R Script
Reference Manual PDF


biocViews GeneExpression, SingleCell, Software
Version 1.16.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 4.0)
Imports SingleCellExperiment(>= 1.8.0), SummarizedExperiment(>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors(>= 0.24.0), igraph, scales, scran(>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions
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Follow Installation instructions to use this package in your R session.

Source Package CiteFuse_1.16.0.tar.gz
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macOS Binary (x86_64) CiteFuse_1.16.0.tgz
macOS Binary (arm64) CiteFuse_1.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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