decontX

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

Decontamination of single cell genomics data

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DOI: 10.18129/B9.bioc.decontX

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0001-9261-6061 , Masanao Yajima [aut] ORCID iD ORCID: 0000-0002-7583-3707 , Joshua Campbell [aut, cre] ORCID iD ORCID: 0000-0003-0780-8662

Maintainer: Joshua Campbell <camp at bu.edu>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")

decontPro HTML R Script

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

Reference Manual PDF

NEWS Text

LICENSE Text

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Details

biocViews Bayesian, SingleCell, Software

Version 1.9.0

In Bioconductor since BioC 3.18 (R-4.3) (2 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

URL

Suggests BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0)

Linking To 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)

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

Source Package decontX_1.9.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

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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/

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