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 (3.21)
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] (ORCID:
Maintainer: Keita Iida <kiida at protein.osaka-u.ac.jp>
citation("ASURAT")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | ASURAT_1.11.0.zip |
| macOS Binary (x86_64) | ASURAT_1.11.0.tgz |
| macOS Binary (arm64) | ASURAT_1.11.0.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 |