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

## Documentation for package ‘CiteFuse’ version 1.25.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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