CiteFuse
This is the released version of CiteFuse; for the devel version, see CiteFuse.
All Bioconductor versions of CiteFuse
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11
CiteFuse: multi-modal analysis of CITE-seq data
Bioconductor version: 3.23 · Package version: 1.24.0
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 sydney.edu.au>
Citation
From within R, enter citation("CiteFuse"):
Yingxin Lin, Hani Kim. CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data. doi:10.18129/B9.bioc.CiteFuse, R package version 1.24.0, https://bioconductor.org/packages/CiteFuse.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CiteFuse")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.24.0 |
| License | GPL-3 |
| Bug Reports | https://github.com/SydneyBioX/CiteFuse/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6 years) |
| Downloads rank | 1064 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/CiteFuse/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CiteFuse")| CiteFuse: getting started | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | CiteFuse_1.24.0.tar.gz |
| Windows binary (x86_64) | CiteFuse_1.24.0.zip |
| macOS binary (arm64) | CiteFuse_1.24.0.tgz |
| macOS binary (x86_64) | CiteFuse_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CiteFuse |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CiteFuse |
| Package Downloads Report | Download Stats |
Dependencies
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
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown
Reverse dependencies
Suggests Me (1): MuData