| 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: | 1.2.2 |
| 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.
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