ASURAT
This is the development version of ASURAT; for the stable release version, see ASURAT.
Functional annotation-driven unsupervised clustering for single-cell data
Bioconductor version: Development (3.24)
ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
Author: Keita Iida [aut, cre]
, Johannes Nicolaus Wibisana [ctb]
Maintainer: Keita Iida <kiida at protein.osaka-u.ac.jp>
citation("ASURAT")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ASURAT")
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("ASURAT")| ASURAT | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, GeneSignaling, Sequencing, SingleCell, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics |
| System Requirements | |
| URL |
See More
| Suggests | ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ASURAT_1.17.0.tar.gz |
| Windows Binary (x86_64) | ASURAT_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | ASURAT_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | ASURAT_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ASURAT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ASURAT |
| Bioc Package Browser | https://code.bioconductor.org/browse/ASURAT/ |
| Package Short Url | https://bioconductor.org/packages/ASURAT/ |
| Package Downloads Report | Download Stats |