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Bioconductor - CiteFuse (development version)

CiteFuse

This is the development version of CiteFuse; for the stable release version, see CiteFuse.

CiteFuse: multi-modal analysis of CITE-seq data

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CiteFuse")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CiteFuse")
Details biocViews GeneExpression, SingleCell, Software Version 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (5 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 System Requirements URL Bug Reports https://github.com/SydneyBioX/CiteFuse/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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