- recipe bioconductor-dropletutils
Utilities for Handling Single-Cell Droplet Data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/DropletUtils.html
- License:
GPL-3
- Recipe:
- Links:
biotools: DropletUtils
Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
- package bioconductor-dropletutils¶
- versions:
1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.14.2-1,1.14.2-0,1.14.0-0,1.12.1-0,1.12.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.14.2-1,1.14.2-0,1.14.0-0,1.12.1-0,1.12.0-0,1.10.3-0,1.10.0-0,1.8.0-0,1.6.1-0,1.4.2-0,1.2.1-0,1.0.3-0- depends bioconductor-beachmat:
>=2.18.0,<2.19.0- depends bioconductor-beachmat:
>=2.18.0,<2.19.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0a0- depends bioconductor-delayedmatrixstats:
>=1.24.0,<1.25.0- depends bioconductor-delayedmatrixstats:
>=1.24.0,<1.25.0a0- depends bioconductor-edger:
>=4.0.0,<4.1.0- depends bioconductor-edger:
>=4.0.2,<4.1.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-hdf5array:
>=1.30.0,<1.31.0- depends bioconductor-hdf5array:
>=1.30.0,<1.31.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rhdf5:
>=2.46.0,<2.47.0- depends bioconductor-rhdf5:
>=2.46.1,<2.47.0a0- depends bioconductor-rhdf5lib:
>=1.24.0,<1.25.0- depends bioconductor-rhdf5lib:
>=1.24.0,<1.25.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-scuttle:
>=1.12.0,<1.13.0- depends bioconductor-scuttle:
>=1.12.0,<1.13.0a0- 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:
- depends r-dqrng:
- depends r-matrix:
- depends r-r.utils:
- depends r-rcpp:
- 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-dropletutils and update with:: mamba update bioconductor-dropletutils
To create a new environment, run:
mamba create --name myenvname bioconductor-dropletutils
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-dropletutils:<tag> (see `bioconductor-dropletutils/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-dropletutils/README.html)
