Package: CiteFuse 1.17.0

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-1.17.0(bioc 3.20)CiteFuse-1.16.0(bioc 3.19)

bioconductor-package

24 exports 0.71 score 155 dependencies 2 mentions

Last updated 2 months agofrom:edba2635f6

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 base64enc bayesm beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster bslib cachem cli cluster codetools colorspace compositions cowplot cpp11 crayon crosstalk curl data.table dbscan DelayedArray DelayedMatrixStats DEoptimR digest dplyr dqrng edgeR evaluate fansi farver fastmap FNN fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime mixtools munsell nlme openssl pheatmap pillar pkgconfig plotly plyr polyclip promises purrr R6 randomForest rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown robustbase RSpectra rsvd Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scran scuttle segmented SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys systemfonts tensorA tibble tidygraph tidyr tidyselect tinytex tweenr UCSC.utils utf8 uwot vctrs viridis viridisLite withr xfun XVector yaml zlibbioc

CiteFuse: getting started

Yingxin Lin, Hani Jieun Kim

Rendered fromCiteFuse.Rmdusingknitr::rmarkdownon Jun 30 2024.

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