recipe bioconductor-dropletutils

Utilities for Handling Single-Cell Droplet Data

Homepage

https://bioconductor.org/packages/3.13/bioc/html/DropletUtils.html

License

GPL-3

Recipe

/bioconductor-dropletutils/meta.yaml

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

1.12.1-0,  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 >=2.8.0,<2.9.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-delayedarray >=0.18.0,<0.19.0

• bioconductor-delayedmatrixstats >=1.14.0,<1.15.0

• bioconductor-edger >=3.34.0,<3.35.0

• bioconductor-hdf5array >=1.20.0,<1.21.0

• bioconductor-rhdf5 >=2.36.0,<2.37.0

• bioconductor-rhdf5lib >=1.14.0,<1.15.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-scuttle >=1.2.0,<1.3.0

• bioconductor-singlecellexperiment >=1.14.0,<1.15.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.3.0

• r-base >=4.1,<4.2.0a0

• r-bh

• r-dqrng

• r-matrix

• r-r.utils

• r-rcpp

Required By

• bioconductor-spaniel

• scxa-plots

• bioconductor-sccb2

• tximport-scripts

• bioconductor-singlecelltk

• r-acidplots

• cell-types-analysis

• dropletutils-scripts

• bioconductor-spatialexperiment

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)