Package: CiteFuse 1.23.0

Yingxin Lin

CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

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.

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

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CiteFuse.pdf |CiteFuse.html✨
CiteFuse/json (API)
NEWS

# Install 'CiteFuse' in R:

install.packages('CiteFuse', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sydneybiox/citefuse/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

CITEseq_example - A subset of ECCITE-seq data
lr_pair_subset - A subset of Ligand Receptor Pairs
sce_control_subset - A SingleCellExperiment of ECCITE-seq data
sce_ctcl_subset - A SingleCellExperiment of ECCITE-seq data

On BioConductor:CiteFuse-1.23.0(bioc 3.23)CiteFuse-1.22.0(bioc 3.22)

singlecell geneexpression bioinformatics single-cell cpp

6.83 score 28 stars 20 scripts 362 downloads 2 mentions 24 exports 150 dependencies

Last updated from:ef26cbae2f. Checks:1 NOTE, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	230
linux-devel-arm64	OK	363
linux-devel-x86_64	OK	445
source / vignettes	OK	391
linux-release-arm64	OK	351
linux-release-x86_64	OK	397
macos-release-arm64	OK	243
macos-release-x86_64	OK	495
macos-oldrel-arm64	OK	236
macos-oldrel-x86_64	OK	599
windows-devel	OK	353
windows-release	OK	345
windows-oldrel	OK	327
wasm-release	OK	196

Exports:CiteFuse crossSampleDoublets DEbubblePlot DEcomparisonPlot DEgenes DEgenesCross geneADTnetwork igraphClustering importanceADT ligandReceptorTest normaliseExprs plotHTO preprocessing readFrom10X reducedDimSNF selectDEgenes spectralClustering visImportance visLigandReceptor visualiseDim visualiseExprs visualiseExprsList visualiseKNN withinSampleDoublets

Dependencies:abind askpass assorthead base64enc bayesm beachmat BH Biobase BiocGenerics biocmake BiocNeighbors BiocParallel BiocSingular bluster bslib cachem cli cluster codetools compositions cowplot cpp11 crosstalk curl data.table dbscan DelayedArray DEoptimR digest dir.expiry dplyr dqrng edgeR evaluate farver fastmap filelock FNN fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggforce ggplot2 ggraph ggrepel ggridges glue graphlayouts gridExtra gtable highr htmltools htmlwidgets httr igraph IRanges irlba isoband jquerylib jsonlite kernlab knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mime mixtools nlme openssl otel pheatmap pillar pkgconfig plotly plyr polyclip promises purrr R6 randomForest rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppProgress reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown robustbase RSpectra rsvd Rtsne S4Arrays S4Vectors S7 sass ScaledMatrix scales scran scuttle segmented Seqinfo SingleCellExperiment sitmo snow SparseArray statmod stringi stringr SummarizedExperiment survival sys systemfonts tensorA tibble tidygraph tidyr tidyselect tinytex tweenr utf8 uwot vctrs viridis viridisLite withr xfun XVector yaml

CiteFuse: getting started

Yingxin Lin, Hani Jieun Kim

Rendered fromCiteFuse.Rmdusingknitr::rmarkdownon Apr 01 2026.

Last update: 2020-04-16
Started: 2019-11-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CiteFuse	CiteFuse
A subset of ECCITE-seq data (control)	CITEseq_example
crossSampleDoublets	crossSampleDoublets
DEbubblePlot	DEbubblePlot
DEcomparisonPlot	DEcomparisonPlot
DEgenes	DEgenes
DEgenesCross	DEgenesCross
geneADTnetwork	geneADTnetwork
igraphClustering	igraphClustering
importanceADT	importanceADT
ligandReceptorTest	ligandReceptorTest
A subset of Ligand Receptor Pairs	lr_pair_subset
normaliseExprs	normaliseExprs
plotHTO	plotHTO
plotHTOSingle	plotHTOSingle
A function to preprocess the list of expression matrix	preprocessing
readFrom10X	readFrom10X
reducedDimSNF	reducedDimSNF
A SingleCellExperiment of ECCITE-seq data	sce_control_subset
A SingleCellExperiment of ECCITE-seq data	sce_ctcl_subset
selectDEgenes	selectDEgenes
spectralClustering	spectralClustering
visImportance	visImportance
visLigandReceptor	visLigandReceptor
visualiseDim	visualiseDim
visualiseExprs	visualiseExprs
visualiseExprsList	visualiseExprsList
visualiseKNN	visualiseKNN
withinSampleDoublets	withinSampleDoublets