decontX
Decontamination of single cell genomics data
Bioconductor version: Release (3.19)
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>
citation("decontX")):
Installation
To install this package, start R (version "4.4") 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")| decontPro | HTML | R Script |
| Estimate and remove cross-contamination from ambient RNA in single-cell data with DecontX | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, SingleCell, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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 |
See More
| 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) |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | decontX_1.2.0.tar.gz |
| Windows Binary (x86_64) | decontX_1.2.0.zip |
| macOS Binary (x86_64) | decontX_1.2.0.tgz |
| macOS Binary (arm64) | decontX_1.2.0.tgz |
| 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 |