README.md

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

scTensor

R package for detection of cell-cell interaction using Non-negative Tensor Decomposition

Installation of Dependent Packages

# CRAN
install.packages(c("RSQLite", "igraph", "plotly", "nnTensor",
    "rTensor", "abind", "plotrix", "heatmaply", "tagcloud",
    "rmarkdown", "knitr", "outliers", "crayon", "checkmate",
    "testthat", "Seurat", "BiocManager"),
    repos="http://cran.r-project.org")

# Bioconductor
library("BiocManager")
BiocManager::install(c("S4Vectors", "reactome.db", "AnnotationDbi",
    "SummarizedExperiment", "SingleCellExperiment", "BiocStyle",
    "biomaRt", "MeSHDbi", "Category", "meshr", "GOstats", "ReactomePA",
    "DOSE", "LRBase.Hsa.eg.db", "MeSH.Hsa.eg.db", "LRBase.Mmu.eg.db",
    "MeSH.Mmu.eg.db", "LRBaseDbi", "Homo.sapiens"),
    suppressUpdates=TRUE)

Installation

git clone https://github.com/rikenbit/scTensor/
R CMD INSTALL scTensor

or type the code below in the R console window

install.packages("devtools", repos="http://cran.r-project.org")
library(devtools)
devtools::install_github("rikenbit/scTensor")

License

Copyright (c) 2018 Koki Tsuyuzaki and Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Reseach Released under the Artistic License 2.0.

Authors

• Koki Tsuyuzaki
• Manabu Ishii
• Itoshi Nikaido

rikenbit/scTensor documentation built on Jan. 28, 2023, noon