CiteFuse

DOI: 10.18129/B9.bioc.CiteFuse  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CiteFuse.

CiteFuse: multi-modal analysis of CITE-seq data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	CiteFuse
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, SingleCell, Software
Version	1.12.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 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
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/SydneyBioX/CiteFuse/issues
Depends On Me
Imports Me
Suggests Me	MuData
Links To Me
Build Report

Package Archives

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

Source Package	CiteFuse_1.12.0.tar.gz
Windows Binary	CiteFuse_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	CiteFuse_1.12.0.tgz
macOS Binary (arm64)	CiteFuse_1.12.0.tgz
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