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scTensor

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


Bioconductor version: Release (3.18)

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 "4.3") 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 2.12.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Artistic-2.0
Depends R (>= 4.1.0)
Imports methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi(>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr(>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2
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Suggests testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
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Package Archives

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

Source Package scTensor_2.12.0.tar.gz
Windows Binary scTensor_2.12.0.zip (64-bit only)
macOS Binary (x86_64) scTensor_2.12.0.tgz
macOS Binary (arm64) scTensor_2.12.0.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