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Bioconductor - ASURAT (development version)

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 (3.22)

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")): 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")
Details biocViews Clustering, GeneExpression, GeneSignaling, Sequencing, SingleCell, Software Version 1.13.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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.

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