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: | 1.0.0 |
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.
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