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: 1.2.2
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_11
git_last_commit: 2f7e6a2
git_last_commit_date: 2020-07-16
Date/Publication: 2020-07-26
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 1.2.2 Index]