Package: iSubGen 1.0.4

Mao Tian

iSubGen: Integrative Subtype Generation

Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.

Authors:Mao Tian [cre], Paul Boutros [aut], Natalie Fox [aut], Dan Knight [ctb]

iSubGen_1.0.4.tar.gz
iSubGen_1.0.4.zip(r-4.7-any)iSubGen_1.0.4.zip(r-4.6-any)iSubGen_1.0.4.zip(r-4.5-any)
iSubGen_1.0.4.tgz(r-4.6-any)iSubGen_1.0.4.tgz(r-4.5-any)
iSubGen_1.0.4.tar.gz(r-4.7-any)iSubGen_1.0.4.tar.gz(r-4.6-any)
iSubGen_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iSubGen/json (API)

# Install 'iSubGen' in R:

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

Bug tracker:https://github.com/uclahs-cds/package-isubgen/issues

On CRAN:

4.70 score 1 stars 3 scripts 329 downloads 11 exports 42 dependencies

Last updated from:7a8f799bad. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	150
source / vignettes	OK	216
linux-release-x86_64	OK	157
macos-release-arm64	OK	103
macos-oldrel-arm64	OK	89
windows-devel	OK	103
windows-release	OK	98
windows-oldrel	OK	102
wasm-release	OK	149

Exports:apply.scaling calculate.cis.matrix calculate.integrative.similarity.matrix calculate.scaling cluster.patients combine.integrative.features create.autoencoder create.autoencoder.irf.matrix load.molecular.aberration.data read.scaling.factors write.scaling.factors

Dependencies:ALL backports base64enc Biobase BiocGenerics cli cluster config ConsensusClusterPlus generics glue here jsonlite keras KernSmooth lattice lifecycle magrittr Matrix philentropy png poorman processx ps R6 rappdirs Rcpp RcppParallel RcppTOML reticulate rlang rprojroot rstudioapi tensorflow tfautograph tfruns tidyselect vctrs whisker withr yaml zeallot

Guide for using ISOpureR

1 Overview | 2 Independent feature reduction | 3 Pairwise similarity matrix | 4 Combine features and create integrative subtypes | 5 Glossary/Acronyms

Rendered fromiSubGenGuide.Rnwusingknitr::knitr_notangle

Last update: 2024-08-23
Started: 2019-05-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Apply scaling factors	apply.scaling
Calculate consensus integrative correlation matrix	calculate.cis.matrix
Calculate integrative similarity matrix	calculate.integrative.similarity.matrix
Calculate scaling factors	calculate.scaling
Clustering to find patient subtypes	cluster.patients
Combine iSubGen integrative features	combine.integrative.features
Create an autoencoder for dimensionality reduction	create.autoencoder
Create matrix of independent reduced features	create.autoencoder.irf.matrix
Load molecular aberration data	load.molecular.aberration.data
Read scaling factors from file	read.scaling.factors
Write scaling factors to file	write.scaling.factors