DeMixT

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

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

Bioconductor version: Development (3.24)

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

Author: Zeya Wang [aut], Shaolong Cao [aut], Liyang Xie [aut], Ruonan Li [cre], Wenyi Wang [aut]

Maintainer: Ruonan Li <RLi10 at mdanderson.org>

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

Zeya Wang, Shaolong Cao, Liyang Xie, Wenyi Wang. DeMixT: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms. doi:10.18129/B9.bioc.DeMixT, R package version 2.1.0, https://bioconductor.org/packages/DeMixT.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

2. DeMixNB: Deconvolution for Sparse Count Data	HTML	R Script
1. DeMixT	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Coverage, GeneExpression, Microarray, Sequencing, Software, StatisticalMethod, TissueMicroarray
Version	2.1.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	GPL-3
Depends	R (>= 4.0.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment
Imports	matrixStats, stats, truncdist, base64enc, ggplot2, KernSmooth, matrixcalc, sva, dendextend, fitdistrplus, pbapply, psych, magrittr, graphics, grDevices, S4Vectors
System Requirements
URL

Suggests	knitr, rmarkdown, calibrate, BiocStyle
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DeMixT_2.1.0.tar.gz
Windows Binary (x86_64)	DeMixT_2.1.0.zip
macOS Binary (big-sur-x86_64)	DeMixT_2.1.0.tgz
macOS Binary (sonoma-arm64)	DeMixT_2.1.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DeMixT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DeMixT
Package Short Url	https://bioconductor.org/packages/DeMixT/
Package Downloads Report	Download Stats