gedepir

Gene Expression DEconvolution PIpeline in R

Package {gedepir} provides practical implementation of recommended guidelines for inference of cell-type proportions from reference-free deconvolution algorithms.

Installation

To build a conda environment :

conda create -n rtmp -c conda-forge r-base r-biocmanager r-devtools r-ggplot2 r-rmarkdown r-dplyr r-cluster r-data.table r-fastica r-clue r-pheatmap 

To install dependencies and get the current version from GitHub:

BiocManager::install(c("NMF","fgsea"))
remotes::install_github("bcm-uga/gedepir")

Usage

Vignette for basic usage is available at : https://bcm-uga.github.io/gedepir/