UNDO: Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

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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.

Author
Niya Wang <wangny@vt.edu>
Date of publication
None
Maintainer
Niya Wang <wangny@vt.edu>
License
GPL-2
Version
1.16.0

View on Bioconductor

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...

Files in this package

UNDO/DESCRIPTION
UNDO/NAMESPACE
UNDO/NEWS
UNDO/R
UNDO/R/UNDO-internal.R
UNDO/R/calc_E1.R
UNDO/R/dimension_reduction.R
UNDO/R/gene_expression_input.R
UNDO/R/marker_gene_selection.R
UNDO/R/mixing_matrix_computation.R
UNDO/R/two_source_deconv.R
UNDO/build
UNDO/build/vignette.rds
UNDO/data
UNDO/data/BiologicalMixMCF7HS27.rda
UNDO/data/NumericalMixMCF7HS27.rda
UNDO/data/NumericalMixingMatrix.rda
UNDO/data/PureMCF7HS27.rda
UNDO/inst
UNDO/inst/doc
UNDO/inst/doc/UNDO-vignette.R
UNDO/inst/doc/UNDO-vignette.Rnw
UNDO/inst/doc/UNDO-vignette.pdf
UNDO/man
UNDO/man/BiologicalMixMCF7HS27.Rd
UNDO/man/NumericalMixMCF7HS27.Rd
UNDO/man/NumericalMixingMatrix.Rd
UNDO/man/PureMCF7HS27.Rd
UNDO/man/UNDO-package.Rd
UNDO/man/calc_E1.Rd
UNDO/man/dimension_reduction.Rd
UNDO/man/gene_expression_input.Rd
UNDO/man/marker_gene_selection.Rd
UNDO/man/mixing_matrix_computation.Rd
UNDO/man/two_source_deconv.Rd
UNDO/vignettes
UNDO/vignettes/UNDO-vignette.Rnw