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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 (3.19)

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 "4.4") 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")
CiteFuse HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, SingleCell, Software
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
Suggests knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me MuData
Links To Me
Build Report Build Report

Package Archives

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

Source Package CiteFuse_1.15.0.tar.gz
Windows Binary CiteFuse_1.15.0.zip
macOS Binary (x86_64) CiteFuse_1.15.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CiteFuse
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CiteFuse
Bioc Package Browser https://code.bioconductor.org/browse/CiteFuse/
Package Short Url https://bioconductor.org/packages/CiteFuse/
Package Downloads Report Download Stats