- recipe bioconductor-scdblfinder
scDblFinder
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/scDblFinder.html
- License:
GPL-3 + file LICENSE
- Recipe:
The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.
- package bioconductor-scdblfinder¶
- versions:
1.16.0-0,1.14.0-0,1.12.0-0,1.8.0-0,1.6.0-0,1.4.0-1,1.4.0-0,1.2.0-0,1.0.0-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocneighbors:
>=1.20.0,<1.21.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocsingular:
>=1.18.0,<1.19.0- depends bioconductor-bluster:
>=1.12.0,<1.13.0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-scater:
>=1.30.0,<1.31.0- depends bioconductor-scran:
>=1.30.0,<1.31.0- depends bioconductor-scuttle:
>=1.12.0,<1.13.0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends r-base:
>=4.3,<4.4.0a0- depends r-igraph:
- depends r-mass:
- depends r-matrix:
- depends r-xgboost:
- 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-scdblfinder and update with:: mamba update bioconductor-scdblfinder
To create a new environment, run:
mamba create --name myenvname bioconductor-scdblfinder
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-scdblfinder:<tag> (see `bioconductor-scdblfinder/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-scdblfinder/README.html)
