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 (3.23)
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("DeMixT")):
Installation
To install this package, start R (version "4.6") 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")| 1. DeMixT | HTML | R Script |
| 2. DeMixNB: Deconvolution for Sparse Count Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Coverage, GeneExpression, Microarray, Sequencing, Software, StatisticalMethod, TissueMicroarray |
| Version | 1.99.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7 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 |
See More
| Suggests | knitr, rmarkdown, calibrate, BiocStyle |
| 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_1.99.0.tar.gz |
| Windows Binary (x86_64) | DeMixT_1.99.0.zip |
| macOS Binary (big-sur-x86_64) | DeMixT_1.99.0.tgz |
| macOS Binary (big-sur-arm64) | DeMixT_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | DeMixT_1.99.0.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 |