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https://github.com/rikenbit/scTensor

R package for detection of cell-cell interaction using Non-negative Tensor Decomposition
https://github.com/rikenbit/scTensor

Last synced: 4 months ago
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R package for detection of cell-cell interaction using Non-negative Tensor Decomposition

Host: GitHub
URL: https://github.com/rikenbit/scTensor
Owner: rikenbit
Created: 2018-05-28T09:36:23.000Z (about 6 years ago)
Default Branch: master
Last Pushed: 2023-01-12T09:46:17.000Z (over 1 year ago)
Last Synced: 2023-12-01T06:00:25.946Z (7 months ago)
Language: R
Size: 18.2 MB
Stars: 32
Watchers: 16
Forks: 6
Open Issues: 1
Metadata Files:
- Readme: README.md

Lists

awesome-cell-cell-communication - scTensor - [R]- scTensor is a R package for detection of cell-cell interaction using Non-negative Tensor Decomposition. (Uncategorized / Uncategorized)

README

        [![DOI](https://zenodo.org/badge/135140761.svg)](https://zenodo.org/badge/latestdoi/135140761)

[![](https://img.shields.io/badge/release%20version-2.6.0-green.svg)](https://www.bioconductor.org/packages/release/bioc/html/scTensor.html)

![GitHub Actions](https://github.com/rikenbit/scTensor/actions/workflows/build_test_push.yml/badge.svg)

# scTensor

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

Installation of Dependent Packages

======

```r

# 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

======

```r

git clone https://github.com/rikenbit/scTensor/

R CMD INSTALL scTensor

```

or type the code below in the R console window

```r

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](http://www.perlfoundation.org/artistic_license_2_0).

## Authors

- Koki Tsuyuzaki

- Manabu Ishii

- Itoshi Nikaido