scTensor-package {scTensor} | R Documentation |
The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.
The DESCRIPTION file:
Package: | scTensor |
Type: | Package |
Title: | Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition |
Version: | 2.4.1 |
Authors@R: | c(person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp"), person("Kozo", "Nishida", role = "aut", email = "kozo.nishida@gmail.com")) |
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 |
Suggests: | testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens |
Description: | The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor. |
License: | Artistic-2.0 |
biocViews: | DimensionReduction, SingleCell, Software, GeneExpression |
VignetteBuilder: | knitr |
git_url: | https://git.bioconductor.org/packages/scTensor |
git_branch: | RELEASE_3_14 |
git_last_commit: | e0462fa |
git_last_commit_date: | 2021-12-16 |
Date/Publication: | 2021-12-19 |
Author: | Koki Tsuyuzaki [aut, cre], Kozo Nishida [aut] |
Maintainer: | Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp> |
Index of help topics:
CCSParams-class Class "CCSParams" GermMale The matrix which is used as test data of scTensor. cellCellDecomp Performing scTensor cellCellRanks Rank estimation of the CCI-tensor cellCellReport HTML report of the result of scTensor cellCellSetting Parameter setting for scTensor cellCellSimulate Parameter Simulate for scTensor getParam Get a parameter labelGermMale The vector contains the celltype information and color scheme of GermMale m The gene-wise mean vector of Quartz-Seq data. newCCSParams New Params scTensor-package Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition setParam Set a parameter tsneGermMale The result of Rtsne against GermMale v The gene-wise variance vector of Quartz-Seq data.
NA
Maintainer: NA
GermMale
,labelGermMale
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tsneGermMale
,cellCellSetting
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cellCellDecomp
,cellCellReport
ls("package:scTensor")