Package: scTensor 2.23.3

Koki Tsuyuzaki

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

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

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

scTensor_2.23.3.tar.gz
scTensor_2.23.3.zip(r-4.7-any)scTensor_2.23.3.zip(r-4.6-any)scTensor_2.23.3.zip(r-4.5-any)
scTensor_2.23.3.tgz(r-4.6-any)scTensor_2.23.3.tgz(r-4.5-any)
scTensor_2.23.3.tar.gz(r-4.7-any)scTensor_2.23.3.tar.gz(r-4.6-any)
scTensor_2.23.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scTensor/json (API)

# Install 'scTensor' in R:

install.packages('scTensor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

GermMale - The matrix which is used as test data of scTensor.
labelGermMale - The vector contains the celltype information and color scheme of GermMale
m - The gene-wise mean vector of Quartz-Seq data.
tsneGermMale - The result of Rtsne against GermMale
v - The gene-wise variance vector of Quartz-Seq data.

On BioConductor:scTensor-2.23.3(bioc 3.24)scTensor-2.22.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dimensionreduction singlecell software geneexpression

2.48 score 5 scripts 527 downloads 1 mentions 9 exports 219 dependencies

Last updated from:9729b3509e. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	406
linux-devel	WARNING	514
source / vignettes	ERROR	617
linux-release	WARNING	533
macos-release	WARNING	361
macos-oldrel	WARNING	434
windows-devel	WARNING	586
windows-release	WARNING	510
windows-oldrel	WARNING	490
wasm-release	OK	348

Exports:BuildSignedCCI cellCellDecomp cellCellRanks cellCellReport cellCellSetting cellCellSimulate getParam newCCSParams setParam<-

Dependencies:abind annotate AnnotationDbi AnnotationForge AnnotationHub ape aplot askpass assertthat backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocStyle BiocVersion Biostrings bit bit64 bitops blob bookdown bslib ca cachem callr Category ccTensor checkmate class classInt cli cluster codetools colorspace commonmark concaveman cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend digest dir.expiry DOSE dotCall64 dplyr e1071 egg enrichit enrichplot entropy evaluate farver fastmap fdrtool fields filelock fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs gclus gdtools genefilter generics GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree glue GO.db GOSemSim GOstats graph graphite graphlayouts gridExtra gridGraphics GSEABase gson gtable heatmaply hexbin highr htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling later lattice lazyeval lifecycle litedown magrittr maps markdown MASS Matrix MatrixGenerics matrixStats memoise MeSHDbi meshr mime misc3d nlme nnTensor openssl otel outliers patchwork pillar pkgconfig plot3D plotly plotrix plyr png polyclip processx promises proxy ps purrr qap R6 RANN rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reactome.db ReactomePA registry reshape2 Rgraphviz rlang rmarkdown RSpectra RSQLite rTensor s2 S4Arrays S4Vectors S7 sass scales scatterpie schex Seqinfo seriation sf SingleCellExperiment spam SparseArray stringi stringr SummarizedExperiment survival sys systemfonts tagcloud tibble tidydr tidygraph tidyr tidyselect tidytree tinytex treeio TSP tweenr units utf8 V8 vctrs Vicus viridis viridisLite visNetwork webshot withr wk xfun XML xtable XVector yaml yulab.utils

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition	scTensor-package scTensor
Build Signed Cell-Cell Interaction Graphs	BuildSignedCCI
Class "CCSParams"	CCSParams-class
Performing scTensor	cellCellDecomp cellCellDecomp,SingleCellExperiment-method
Rank estimation of the CCI-tensor	cellCellRanks cellCellRanks,SingleCellExperiment-method
HTML report of the result of scTensor	cellCellReport cellCellReport,SingleCellExperiment-method
Parameter setting for scTensor	cellCellSetting cellCellSetting,SingleCellExperiment-method
Parameter Simulate for scTensor	cellCellSimulate cellCellSimulate,SingleCellExperiment-method
The matrix which is used as test data of scTensor.	GermMale
Get a parameter	getParam getParam,CCSParams-method
The vector contains the celltype information and color scheme of GermMale	labelGermMale
The gene-wise mean vector of Quartz-Seq data.	m
New Params	newCCSParams
Set a parameter	setParam setParam,CCSParams,ANY-method setParam,CCSParams-method setParam<- setParam<-,CCSParams,ANY-method setParam<-,CCSParams-method
The result of Rtsne against GermMale	tsneGermMale
The gene-wise variance vector of Quartz-Seq data.	v