scTensor
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Bioconductor version: Release (3.20)
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 "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, GeneExpression, SingleCell, Software |
| Version | 2.16.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub |
| Linking To | |
| 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.
| Source Package | scTensor_2.16.0.tar.gz |
| Windows Binary (x86_64) | scTensor_2.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | scTensor_2.16.0.tgz |
| macOS Binary (arm64) | scTensor_2.16.0.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 |