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This is the development version of decontX; for the stable release version, see decontX.

Decontamination of single cell genomics data

Bioconductor version: Development (3.20)

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

Author: Yuan Yin [aut, cre] , Masanao Yajima [aut] , Joshua Campbell [aut]

Maintainer: Yuan Yin <yuan_yin at>

Citation (from within R, enter citation("decontX")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

decontPro HTML R Script
Estimate and remove cross-contamination from ambient RNA in single-cell data with DecontX HTML R Script
Reference Manual PDF


biocViews Bayesian, SingleCell, Software
Version 1.3.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr
System Requirements GNU make
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Suggests BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0)
Linking To BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>=, RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
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Follow Installation instructions to use this package in your R session.

Source Package decontX_1.3.0.tar.gz
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macOS Binary (x86_64) decontX_1.3.0.tgz
macOS Binary (arm64) decontX_1.3.0.tgz
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Source Repository (Developer Access) git clone
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