CiteFuse

This is the released version of CiteFuse; for the devel version, see CiteFuse.

CiteFuse: multi-modal analysis of CITE-seq data

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DOI: 10.18129/B9.bioc.CiteFuse

Bioconductor version: Release (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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, SingleCell, Software

Version 1.22.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

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_1.22.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) CiteFuse_1.22.0.tgz

macOS Binary (arm64) CiteFuse_1.22.0.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/

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