scTGIF-package {scTGIF} | R Documentation

## Cell type annotation for unannotated single-cell RNA-Seq data

### Description

scTGIF connects the cells and the related gene functions without cell type label.

### Details

The DESCRIPTION file:

Package: | scTGIF
Type: | Package
Title: | Cell type annotation for unannotated single-cell RNA-Seq data
Version: | 1.1.0
Authors@R: | person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp")
Depends: | R (>= 3.6.0)
Imports: | GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr
Suggests: | testthat
Description: | scTGIF connects the cells and the related gene functions without cell type label.
License: | Artistic-2.0
biocViews: | DimensionReduction, QualityControl, SingleCell, Software, GeneExpression
VignetteBuilder: | knitr
git_url: | https://git.bioconductor.org/packages/scTGIF
git_branch: | master
git_last_commit: | 1e94149
git_last_commit_date: | 2019-10-29
Date/Publication: | 2019-11-08
Author: | Koki Tsuyuzaki [aut, cre]
Maintainer: | Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>

Index of help topics:

    DistalLungEpithelium    Gene expression matrix of DistalLungEpithelium
                            dataset containing five cluster.
    calcTGIF                Function for connecting cellular patterns and
                            functional patterns using jNMF
    label.DistalLungEpithelium
                            Cellular label of DistalLungEpithelium dataset
                            containing five cluster.
    pca.DistalLungEpithelium
                            The result of PCA of the DistalLungEpithelium
                            dataset.
    reportTGIF              Function for reporting the result of 'calcTGIF'
                            function
    scTGIF-package          Cell type annotation for unannotated
                            single-cell RNA-Seq data
    settingTGIF             Paramter setting for scTGIF

`calcTGIF` function calculates what kind of cellular patterns and functional patterns are contained in single-cell RNA-seq data and `reportTGIF` function generates report of analytic result. The algorithm is based on joint NMF, which is implemented in nnTensor package.

### Author(s)

NA

Maintainer: NA

### References

Dominic Grun, Anna Lyubimova, Lennart Kester, Kay Wiebrands, Onur Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden (2015) Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature, 525: 251-255

[Package scTGIF version 1.1.0 Index]