scTGIF-package {scTGIF} | R Documentation |
scTGIF connects the cells and the related gene functions without cell type label.
The DESCRIPTION file:
Package: | scTGIF |
Type: | Package |
Title: | Cell type annotation for unannotated single-cell RNA-Seq data |
Version: | 1.7.0 |
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: | master |
git_last_commit: | 6bfbed9 |
git_last_commit_date: | 2021-05-19 |
Date/Publication: | 2021-06-06 |
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.
NA
Maintainer: NA
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