- recipe bioconductor-decontx
Decontamination of single cell genomics data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/decontX.html
- License:
MIT + file LICENSE
- Recipe:
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.
- package bioconductor-decontx¶
- versions:
1.0.0-0- depends bioconductor-celda:
>=1.18.0,<1.19.0- depends bioconductor-celda:
>=1.18.1,<1.19.0a0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-scater:
>=1.30.0,<1.31.0- depends bioconductor-scater:
>=1.30.1,<1.31.0a0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-bh:
>=1.66.0- depends r-dbscan:
- depends r-ggplot2:
- depends r-matrix:
>=1.5.3- depends r-mcmcprecision:
- depends r-patchwork:
- depends r-plyr:
- depends r-rcpp:
>=0.12.0- depends r-rcppeigen:
>=0.3.3.3.0- depends r-rcppparallel:
>=5.0.1- depends r-reshape2:
- depends r-rstan:
>=2.18.1- depends r-rstantools:
>=2.2.0- depends r-seurat:
- depends r-stanheaders:
>=2.18.0- depends r-withr:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-decontx and update with:: mamba update bioconductor-decontx
To create a new environment, run:
mamba create --name myenvname bioconductor-decontx
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-decontx:<tag> (see `bioconductor-decontx/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-decontx/README.html)
