ASURAT

This is the development version of ASURAT; for the stable release version, see ASURAT.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

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] ORCID: 0000-0002-1076-830X , Johannes Nicolaus Wibisana [ctb]

Maintainer: Keita Iida <kiida at protein.osaka-u.ac.jp>

Citation (from within R, enter citation("ASURAT")):

Keita Iida. ASURAT: Functional annotation-driven unsupervised clustering for single-cell data. doi:10.18129/B9.bioc.ASURAT, R package version 1.17.0, https://bioconductor.org/packages/ASURAT.

Generated from the package metadata; it may differ from the package's own citation.

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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

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

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, r-universe

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 (64-bit only)
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
Package Short Url	https://bioconductor.org/packages/ASURAT/
Package Downloads Report	Download Stats