scTensor-package {scTensor} | R Documentation |
The algorithm is based on the non-negative tucker decomposition (NTD) of nnTensor.
The DESCRIPTION file:
Package: | scTensor |
Type: | Package |
Title: | Detection of cell-cell interaction within single-cell RNA-Seq data |
Version: | 1.0.0 |
Date: | 2018-11-06 |
Authors@R: | person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp") |
Depends: | R (>= 3.5.0) |
Imports: | methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, biomaRt, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate |
Suggests: | testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi |
Description: | The algorithm is based on the non-negative tucker decomposition (NTD) of nnTensor. |
License: | Artistic-2.0 |
biocViews: | DimensionReduction, SingleCell |
VignetteBuilder: | knitr |
git_url: | https://git.bioconductor.org/packages/scTensor |
git_branch: | RELEASE_3_9 |
git_last_commit: | 593b9b6 |
git_last_commit_date: | 2019-05-02 |
Date/Publication: | 2019-05-02 |
Author: | Koki Tsuyuzaki [aut, cre] |
Maintainer: | Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp> |
Index of help topics:
.m The gene-wise mean vector of Quartz-Seq data. .v The gene-wise variance vector of Quartz-Seq data. 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 newCCSParams New Params scTensor-package Detection of cell-cell interaction within single-cell RNA-Seq data setParam Set a parameter tsneGermMale The result of Rtsne against GermMale
NA
Maintainer: NA
GermMale
,labelGermMale
,
tsneGermMale
,cellCellSetting
,
cellCellDecomp
,cellCellReport
if(interactive()){ # Package Loading library(SingleCellExperiment) library(LRBase.Hsa.eg.db) # Data Loading data(GermMale) data(labelGermMale) data(tsneGermMale) # SingleCellExperiment-class sce <- SingleCellExperiment(assays = list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y) # Setting cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) # Decomposition cellCellDecomp(sce, ranks=c(4,4,5)) # Report tmp <- tempdir() cellCellReport(sce, reducedDimNames="TSNE", out.dir=tmp, html.open = TRUE, title="Cell-cell interaction within Germline, Male, GSE86146", author="Koki Tsuyuzaki", thr=5) }else{ ls("package:scTensor") }