DeMixT

This package is for version 3.17 of Bioconductor; for the stable, up-to-date 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: 3.17

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 "4.3") and enter:


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

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 1.16.0
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
System Requirements
URL
See More
Suggests
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DeMixT_1.16.0.tar.gz
Windows Binary DeMixT_1.16.0.zip
macOS Binary (x86_64) DeMixT_1.16.0.tgz
macOS Binary (arm64) DeMixT_1.16.0.tgz
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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive