scTensor
This is the development version of scTensor; for the stable release version, see scTensor.
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Bioconductor version: Development (3.24)
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("scTensor")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 2.23.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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 |
| 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_2.23.0.tar.gz |
| Windows Binary (x86_64) | scTensor_2.23.0.zip |
| macOS Binary (big-sur-x86_64) | scTensor_2.23.0.tgz |
| macOS Binary (sonoma-arm64) | scTensor_2.23.0.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 |