decontX

Methods for decontamination of single cell data. This package implements both DecontX (Yang et al., 2020) for single-cell RNA-seq data and DecontPro (Yin et al., 2023) for single-cell protein expression data.

Installation Instructions

You can install the package through Bioconductor with:

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

BiocManager::install("decontX")

Alternatively, install the development version through GitHub using devtools package:

# install.packages("devtools")
devtools::install_github("campbio/decontX")

Vignettes

Vignettes are available on Bioconductor.

To build vignette when installing from GitHub, add the flag build_vignettes = TRUE:

library(devtools)
install_github("campbio/decontX", build_vignettes = TRUE)

Then vignettes can be accessed through:

vignette('decontX', package = 'decontX')
vignette('decontPro', package = 'decontX')