CiteFuse
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see CiteFuse.
CiteFuse: multi-modal analysis of CITE-seq data
Bioconductor version: 3.18
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 "4.3") 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")| CiteFuse | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, SingleCell, Software |
| Version | 1.14.0 |
| 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_1.14.0.tar.gz |
| Windows Binary | CiteFuse_1.14.0.zip |
| macOS Binary (x86_64) | CiteFuse_1.14.0.tgz |
| macOS Binary (arm64) | CiteFuse_1.14.0.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 |