Package: UNDO 1.55.0

Niya Wang

UNDO: Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.

Authors:Niya Wang <[email protected]>

UNDO_1.55.0.tar.gz
UNDO_1.55.0.zip(r-4.7)UNDO_1.55.0.zip(r-4.6)UNDO_1.55.0.zip(r-4.5)
UNDO_1.55.0.tgz(r-4.6-any)UNDO_1.55.0.tgz(r-4.5-any)
UNDO_1.55.0.tar.gz(r-4.7-any)UNDO_1.55.0.tar.gz(r-4.6-any)
UNDO_1.55.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
UNDO/json (API)

# Install 'UNDO' in R:

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

Datasets:

BiologicalMixMCF7HS27 - MCF7 and HS27 biologically mixed
NumericalMixingMatrix - Mixing matrix of data NumericalMixMCF7HS27
NumericalMixMCF7HS27 - MCF7 and HS27 numerically mixed
PureMCF7HS27 - Pure MCF7 and HS27

On BioConductor:UNDO-1.55.0(bioc 3.24)UNDO-1.54.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software

4.00 score 10 scripts 444 downloads 5 mentions 6 exports 6 dependencies

Last updated from:69dc913419. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	149
linux-devel-x86_64	OK	240
source / vignettes	OK	166
linux-release-x86_64	OK	133
macos-release-arm64	OK	95
macos-oldrel-arm64	OK	77
windows-devel	OK	69
windows-release	OK	66
windows-oldrel	OK	88
wasm-release	OK	94

Exports:calc_E1 dimension_reduction gene_expression_input marker_gene_selection mixing_matrix_computation two_source_deconv

Dependencies:Biobase BiocGenerics boot generics MASS nnls

UNDO Usage

Rendered fromUNDO-vignette.Rnwusingutils::Sweave

Last update: 2014-07-17
Started: 2014-03-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Implementation of UNDO (unsupervised deconvolution of tumor-stromal mixed expressions)	UNDO-package UNDO
MCF7 and HS27 biologically mixed	BiologicalMixMCF7HS27
function calculating the E1 measurement	calc_E1
Dimension reduction function	dimension_reduction
Detect whether the input gene expression data are valid	gene_expression_input
Select marker genes in two sources	marker_gene_selection
Calculate and scale the mixing matrix	mixing_matrix_computation
mixing matrix of data NumericalMixMCF7HS27	NumericalMixingMatrix
MCF7 and HS27 numerically mixed	NumericalMixMCF7HS27
pure MCF7 and HS27	PureMCF7HS27
Main function to call other subfunction to deconvolute the mixed expression data.	two_source_deconv