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DeMixT

This is the development version of DeMixT; for the stable release version, see DeMixT.

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms


Bioconductor version: Development (3.19)

DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.

Author: Zeya Wang <zw17.rice at gmail.com>, Shaolong Cao<scao at mdanderson.org>, Wenyi Wang <wwang7 at at mdanderson.org>

Maintainer: Shuai Guo <shuai.guo at uth.tmc.edu>

Citation (from within R, enter citation("DeMixT")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DeMixT")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DeMixT")
DeMixT.Rmd HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Coverage, GeneExpression, Microarray, Sequencing, Software, StatisticalMethod, TissueMicroarray
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3
Depends R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva
Imports matrixStats, stats, truncdist, base64enc, ggplot2
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DeMixT_1.19.0.tar.gz
Windows Binary DeMixT_1.19.0.zip
macOS Binary (x86_64) DeMixT_1.19.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/DeMixT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DeMixT
Bioc Package Browser https://code.bioconductor.org/browse/DeMixT/
Package Short Url https://bioconductor.org/packages/DeMixT/
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