decontX

DOI: 10.18129/B9.bioc.decontX  

Decontamination of single cell genomics data

Bioconductor version: Release (3.18)

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 outlook.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("decontX")

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

Documentation

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

browseVignettes("decontX")

 

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

Details

biocViews	Bayesian, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
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
LinkingTo	BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests	BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0)
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	decontX_1.0.0.tar.gz
Windows Binary	decontX_1.0.0.zip
macOS Binary (x86_64)	decontX_1.0.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/decontX
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/decontX
Bioc Package Browser	https://code.bioconductor.org/browse/decontX/
Package Short Url	https://bioconductor.org/packages/decontX/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive