Bioconductor - decontX

Bioconductor - decontX
Bioconductor 3.22
Software Packages
decontX
decontX
This is the
released
version of decontX; for the devel version, see
decontX
Decontamination of single cell genomics data
DOI:
10.18129/B9.bioc.decontX
Bioconductor version:
Release (3.22)
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: 0000-0001-9261-6061
, Masanao Yajima [aut]
ORCID: 0000-0002-7583-3707
, Joshua Campbell [aut, cre]
ORCID: 0000-0003-0780-8662
Maintainer:
Joshua Campbell
Citation (from within R, enter
citation("decontX")
):
Installation
To install this package, start R (version "4.5") 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
PDF
NEWS
Text
LICENSE
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
Bayesian
SingleCell
Software
Version
1.8.0
In Bioconductor since
BioC 3.18 (R-4.3) (2.5 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
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_1.8.0.tar.gz
Windows Binary (x86_64)
decontX_1.8.0.zip
macOS Binary (x86_64)
decontX_1.8.0.tgz
macOS Binary (arm64)
decontX_1.8.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/decontX
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/decontX
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