DeMixT

DOI: 10.18129/B9.bioc.DeMixT  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	DeMixT.Rmd
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Coverage, GeneExpression, Microarray, Sequencing, Software, StatisticalMethod, TissueMicroarray
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 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
LinkingTo	Rcpp
Suggests
SystemRequirements
Enhances
URL
Depends On Me
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Build Report

Package Archives

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

Source Package	DeMixT_1.14.0.tar.gz
Windows Binary	DeMixT_1.14.0.zip (64-bit only)
macOS Binary (x86_64)	DeMixT_1.14.0.tgz
macOS Binary (arm64)	DeMixT_1.14.0.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