This package contains methods and utilities for performing gene expression deconvolution, i.e. estimating cell type proportions and/or cell-specific gene expression signatures from global expression data in heterogeneous samples. Its main objectives are to provide:
- a unified base framework for applying and developing deconvolution analysis;
- a user-friendly and intuitive interface;
- a resource of relevant auxiliary data such as benchmark datasets or cell marker gene lists.
See Algorithms for a list of all available deconvolution methods.
# install biocLite if not already there
if( !require(BiocInstaller) ){
# enable Bioconductor repositories
# -> add Bioc-software
setRepositories()
install.packages('BiocInstaller')
library(BiocInstaller)
}
# or alternatively do:
# source('http://www.bioconductor.org/biocLite.R')
# install (NB: this might ask you to update some of your packages)
biocLite('CellMix', siteRepos = 'http://web.cbio.uct.ac.za/~renaud/CRAN', type='both')