recipe bioconductor-phantasuslite

Loading and annotation RNA-Seq counts matrices

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/phantasusLite.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-phantasuslite/meta.yaml

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

package bioconductor-phantasuslite

(downloads) docker_bioconductor-phantasuslite

versions:

1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-rhdf5client:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-httr:

depends r-stringr:

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-phantasuslite

and update with::

   mamba update bioconductor-phantasuslite

To create a new environment, run:

mamba create --name myenvname bioconductor-phantasuslite

with myenvname being 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-phantasuslite:<tag>

(see `bioconductor-phantasuslite/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda 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-phantasuslite/README.html)