<!-- README.md is generated from README.Rmd. Please edit that file --> # decontX <!-- badges: start --> [](https://github.com/campbio/decontX/actions/workflows/R-CMD-check.yaml) [](https://codecov.io/gh/campbio/decontX) <!-- badges: end --> Methods for decontamination of single cell data. This package implements both DecontX (Yang et al., [2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1950-6)) for single-cell RNA-seq data and DecontPro (Yin et al., [2023](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1032/7420100)) for single-cell protein expression data. ## Installation Instructions You can install the package through [Bioconductor](https://bioconductor.org/packages/decontX) with: ``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("decontX") ``` Alternatively, install the development version through [GitHub](https://github.com/campbio/decontX) using `devtools` package: ``` r # install.packages("devtools") devtools::install_github("campbio/decontX") ``` ## Vignettes Vignettes are available on [Bioconductor](https://bioconductor.org/packages/decontX). To build vignette when installing from GitHub, add the flag `build_vignettes = TRUE`: ``` r library(devtools) install_github("campbio/decontX", build_vignettes = TRUE) ``` Then vignettes can be accessed through: ``` r vignette('decontX', package = 'decontX') vignette('decontPro', package = 'decontX') ```