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CiteFuse
This is thedevelopment version of CiteFuse; for the stable release version, seeCiteFuse.
CiteFuse: multi-modal analysis of CITE-seq data
Bioconductor version: Development (3.23)
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("CiteFuse")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("CiteFuse")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression,SingleCell,Software |
| Version | 1.23.0 |
| 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | CiteFuse_1.23.0.tar.gz |
| Windows Binary (x86_64) | CiteFuse_1.23.0.zip |
| macOS Binary (x86_64) | |
| 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 |