UNDO: Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
Version 1.18.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorNiya Wang <wangny@vt.edu>
Bioconductor views Software
Date of publicationNone
MaintainerNiya Wang <wangny@vt.edu>
LicenseGPL-2
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("UNDO")

Man pages

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

Functions

BiologicalMixMCF7HS27 Man page
NumericalMixMCF7HS27 Man page
NumericalMixingMatrix Man page
PureMCF7HS27 Man page
UNDO Man page
UNDO-package Man page
calc_E1 Man page Source code
dimension_reduction Man page Source code
gene_expression_input Man page Source code
marker_gene_selection Man page Source code
mixing_matrix_computation Man page Source code
two_source_deconv Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/UNDO-internal.R
R/calc_E1.R
R/dimension_reduction.R
R/gene_expression_input.R
R/marker_gene_selection.R
R/mixing_matrix_computation.R
R/two_source_deconv.R
build
build/vignette.rds
data
data/BiologicalMixMCF7HS27.rda
data/NumericalMixMCF7HS27.rda
data/NumericalMixingMatrix.rda
data/PureMCF7HS27.rda
inst
inst/doc
inst/doc/UNDO-vignette.R
inst/doc/UNDO-vignette.Rnw
inst/doc/UNDO-vignette.pdf
man
man/BiologicalMixMCF7HS27.Rd
man/NumericalMixMCF7HS27.Rd
man/NumericalMixingMatrix.Rd
man/PureMCF7HS27.Rd
man/UNDO-package.Rd
man/calc_E1.Rd
man/dimension_reduction.Rd
man/gene_expression_input.Rd
man/marker_gene_selection.Rd
man/mixing_matrix_computation.Rd
man/two_source_deconv.Rd
vignettes
vignettes/UNDO-vignette.Rnw
UNDO documentation built on May 20, 2017, 9:25 p.m.