Package: TDbasedUFEadv 1.5.0

Y-h. Taguchi

TDbasedUFEadv: Advanced package of tensor decomposition based unsupervised feature extraction

This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

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

TDbasedUFEadv_1.5.0.tar.gz
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TDbasedUFEadv.pdf |TDbasedUFEadv.html✨
TDbasedUFEadv/json (API)
NEWS

# Install 'TDbasedUFEadv' in R:

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

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

On BioConductor:TDbasedUFEadv-1.5.0(bioc 3.20)TDbasedUFEadv-1.4.0(bioc 3.19)

bioconductor-package

11 exports 0.36 score 211 dependencies

Last updated 2 months agofrom:3b6739aa01

Exports:computeSVD prepareCondDrugandDisease prepareCondTCGA prepareexpDrugandDisease prepareTensorfromList prepareTensorfromMatrix prepareTensorRect selectFeatureProj selectFeatureRect selectFeatureTransRect transSVD

Dependencies:abind AnnotationDbi ape aplot askpass assertthat backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot broom bslib cachem car carData caTools chron cli clipr codetools colorspace commonmark corrplot cowplot cpp11 crayon curl data.table DBI Deriv digest doBy DOSE dplyr enrichplot enrichR evaluate exactRankTests fansi farver fastmap fastmatch fgsea fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggsci ggsignif ggtext ggthemes ggtree glue GO.db GOSemSim gplots graphlayouts gridExtra gridGraphics gridtext gsubfn gtable gtools hash HDO.db highr hms htmltools httpuv httr igraph IRanges isoband jpeg jquerylib jsonlite KEGGREST KernSmooth km.ci KMsurv knitr labeling lambda.r later lattice lazyeval lifecycle lme4 magrittr markdown MASS Matrix MatrixModels maxstat memoise mgcv microbenchmark mime minqa modelr MOFAdata munsell mvtnorm nlme nloptr nnet numDeriv openssl patchwork pbkrtest pillar pkgconfig plogr plotrix plyr png polyclip polynom prettyunits progress promises proto purrr quantreg qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr reshape2 rjson rlang rmarkdown RSQLite rstatix RTCGA rTensor rvest S4Vectors sass scales scatterpie selectr shadowtext shiny snow sourcetools SparseM sqldf STRINGdb stringi stringr survival survminer survMisc sys systemfonts TDbasedUFE tibble tidygraph tidyr tidyselect tidytree tinytex treeio tweenr tximport tximportData tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr WriteXLS xfun XML xml2 xtable XVector yaml yulab.utils zlibbioc zoo

Enrichment

Y-h. Taguchi

Rendered fromEnrichment.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-03-24
Started: 2023-02-06

Explanation of TDbasedUFEadv

Y-h. Taguchi

Rendered fromExplanation_of_TDbasedUFEadv.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-03-22
Started: 2023-03-20

How to use TDbasedUFEadv

Y-h. Taguchi

Rendered fromHow_to_use_TDbasedUFEadv.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-03-24
Started: 2023-03-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Title Perform SVD toward reduced matrix generated from a tensor with partial summation	computeSVD
Prepare condition matrix for expDrug	prepareCondDrugandDisease
Prepare Sample label for TCGA data	prepareCondTCGA
Generating gene expression of drug treated cell lines and a disease cell line	prepareexpDrugandDisease
Prepare tensor from a list that includes multiple profiles	prepareTensorfromList
Generate tensor from two matrices	prepareTensorfromMatrix
Prepare tensor generated from two matrices that share samples	prepareTensorRect
Select feature when projection strategy is employed for the case where features are shared with multiple omics profiles	selectFeatureProj
Select features through the selection of singular value vectors	selectFeatureRect
Select features for a tensor generated from two matrices that share samples.	selectFeatureTransRect
Class definitions	TensorRect-class
Convert SVD to that for the case where samples are shared between two matrices	transSVD

Package: TDbasedUFEadv 1.5.0

TDbasedUFEadv: Advanced package of tensor decomposition based unsupervised feature extraction

Enrichment

Explanation of TDbasedUFEadv

How to use TDbasedUFEadv

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)