recipe bioconductor-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, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

Homepage:https://bioconductor.org/packages/3.8/bioc/html/DropletUtils.html License:GPL-3 Recipe:/bioconductor-dropletutils/meta.yaml Links:biotools: DropletUtils

package bioconductor-dropletutils

Versions:

1.2.1-0, 1.0.3-0

Depends:

• bioconductor-beachmat >=1.4.0,<1.5.0
• bioconductor-biocparallel >=1.16.0,<1.17.0
• bioconductor-edger >=3.24.0,<3.25.0
• bioconductor-hdf5array >=1.10.0,<1.11.0
• bioconductor-rhdf5 >=2.26.0,<2.27.0
• bioconductor-rhdf5lib >=1.4.0,<1.5.0
• bioconductor-s4vectors >=0.20.0,<0.21.0
• bioconductor-singlecellexperiment >=1.4.0,<1.5.0
• libgcc-ng >=7.3.0
• libstdcxx-ng >=7.3.0
• r-base >=3.5.1,<3.5.2.0a0
• r-matrix
• r-rcpp

Required By:

• dropletutils-scripts
• tximport-scripts

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-dropletutils

and update with:

conda update bioconductor-dropletutils

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-dropletutils:<tag>

(see bioconductor-dropletutils/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-dropletutils/README.html)