# decontX \[!\[R-CMD-check\](https://github.com/campbio/decontX/actions/workflows/R-CMD-check.yaml/badge.svg)\](https://github.com/campbio/decontX/actions/workflows/R-CMD-check.yaml) \[!\[codecov\](https://codecov.io/gh/campbio/decontX/graph/badge.svg?token=z5YnsXuWqh)\](https://codecov.io/gh/campbio/decontX) 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') \`\`\`