Package: TDbasedUFE 1.12.0

Y-h. Taguchi

TDbasedUFE: Tensor Decomposition Based Unsupervised Feature Extraction

This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets.

Authors:Y-h. Taguchi [aut, cre]

TDbasedUFE_1.12.0.tar.gz
TDbasedUFE_1.12.0.zip(r-4.7)TDbasedUFE_1.12.0.zip(r-4.6)TDbasedUFE_1.12.0.zip(r-4.5)
TDbasedUFE_1.12.0.tgz(r-4.6-any)TDbasedUFE_1.12.0.tgz(r-4.5-any)
TDbasedUFE_1.12.0.tar.gz(r-4.7-any)TDbasedUFE_1.12.0.tar.gz(r-4.6-any)
TDbasedUFE_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TDbasedUFE/json (API)

# Install 'TDbasedUFE' in R:

install.packages('TDbasedUFE', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tagtag/tdbasedufe/issues

On BioConductor:TDbasedUFE-1.13.0(bioc 3.24)TDbasedUFE-1.12.0(bioc 3.23)

geneexpression featureextraction methylationarray singlecell bioinformatics dna-methylation gene-expression-profiles histone-modifications multiomics tensor-decomposition

5.68 score 5 stars 1 packages 16 scripts 290 downloads 11 exports 57 dependencies

Last updated from:1763056839 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	207
linux-devel-x86_64	OK	317
source / vignettes	OK	258
linux-release-x86_64	OK	253
macos-release-arm64	OK	138
macos-oldrel-arm64	OK	171
windows-devel	OK	168
windows-release	OK	172
windows-oldrel	OK	177
wasm-release	OK	179

Exports:computeHosvd computeHosvdSqure convertSquare PrepareSummarizedExperimentTensor PrepareSummarizedExperimentTensorSquare selectFeature selectFeatureSquare selectSingularValueVectorLarge selectSingularValueVectorSmall tableFeatures tableFeaturesSquare

Dependencies:base64enc BiocGenerics bit bit64 bslib cachem cli clipr commonmark cpp11 crayon digest fastmap fontawesome fs generics GenomicRanges glue hms htmltools httpuv IRanges jquerylib jsonlite later lifecycle magrittr memoise mime MOFAdata otel pillar pkgconfig prettyunits progress promises R6 rappdirs Rcpp readr rlang rTensor S4Vectors sass Seqinfo shiny sourcetools tibble tidyselect tximport tximportData tzdb utf8 vctrs vroom withr xtable

QuickStart

Rendered fromQuickStart.Rmdusingknitr::rmarkdown

Last update: 2023-03-19
Started: 2023-01-21

TDbasedUFE

Rendered fromTDbasedUFE.Rmdusingknitr::rmarkdown

Last update: 2023-03-19
Started: 2023-01-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Title Compute higher order singular value decomposition	computeHosvd
Title Compute higher order singular value decomposition from the tensor generated from squared matrix	computeHosvdSqure
Generate squared tensor from multiomics data	convertSquare
Title Generate feature values formatted as a tensor format	PrepareSummarizedExperimentTensor
Title Generate feature values formatted as a tensor format from Squared matrix	PrepareSummarizedExperimentTensorSquare
Title Select features	selectFeature
Title Select features (for tensor generated from squared matrix)	selectFeatureSquare
Title Select singular value vectors from HOSVD (boxplot version)	selectSingularValueVectorLarge
Title Select singular value vectors from HOSVD	selectSingularValueVectorSmall
Title Show selected features as Table	tableFeatures
Title Show selected features as Table (for Squared one)	tableFeaturesSquare