CiteFuse
This is the released version of CiteFuse; for the devel version, see CiteFuse.
CiteFuse: multi-modal analysis of CITE-seq data
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | CiteFuse_1.24.0.tar.gz |
| Windows Binary (x86_64) | CiteFuse_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | CiteFuse_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | CiteFuse_1.24.0.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 |