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ASURAT

Functional annotation-driven unsupervised clustering for single-cell data


Bioconductor version: Release (3.18)

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

Details

biocViews Clustering, GeneExpression, GeneSignaling, Sequencing, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ASURAT_1.6.0.tar.gz
Windows Binary ASURAT_1.6.0.zip (64-bit only)
macOS Binary (x86_64) ASURAT_1.6.0.tgz
macOS Binary (arm64) ASURAT_1.6.0.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