scTensor

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scTensor.

Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition


Bioconductor version: 3.12

The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.

Author: Koki Tsuyuzaki [aut, cre], Kozo Nishida [aut]

Maintainer: Koki Tsuyuzaki <k.t.the-answer at hotmail.co.jp>

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

Installation

To install this package, start R (version "4.0") and enter:


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

BiocManager::install("scTensor")

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("scTensor")
scTensor HTML R Script
scTensor: 1. Data format and ID conversion HTML R Script
scTensor: 2. Interpretation of HTML report HTML R Script
scTensor: 3. Simulation of CCI HTML R Script
scTensor: 4. Reanalysis of the results of scTensor HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DimensionReduction, GeneExpression, SingleCell, Software
Version 2.0.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2
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Suggests testthat, LRBase.Hsa.eg.db, LRBase.Mmu.eg.db, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
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Build Report Build Report

Package Archives

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

Source Package scTensor_2.0.0.tar.gz
Windows Binary scTensor_2.0.0.zip
macOS 10.13 (High Sierra) scTensor_2.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scTensor
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scTensor
Bioc Package Browser https://code.bioconductor.org/browse/scTensor/
Package Short Url https://bioconductor.org/packages/scTensor/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive