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: | 1.4.0
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, schex, tibble, ggplot2, igraph
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: | RELEASE_3_12
git_last_commit: | f21027e
git_last_commit_date: | 2020-10-27
Date/Publication: | 2020-10-27
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
    cellMarkerToGmt         A function to convert the CellMarker data to
                            GMT files.
    convertRowID            A function to change the row names of a matrix.
    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 1.4.0 Index]