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: 1.0.0
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: RELEASE_3_10
git_last_commit: 5e82bd9
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
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 1.0.0 Index]