recipe bioconductor-gemma.r

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/gemma.R.html

License:

Apache License (>= 2)

Recipe:

/bioconductor-gemma.r/meta.yaml

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

package bioconductor-gemma.r

versions:

2.0.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-bit64:

depends r-data.table:

depends r-digest:

depends r-glue:

depends r-httr:

depends r-jsonlite:

depends r-lubridate:

depends r-magrittr:

depends r-memoise:

depends r-rappdirs:

depends r-rlang:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-gemma.r

and update with::

   mamba update bioconductor-gemma.r

To create a new environment, run:

mamba create --name myenvname bioconductor-gemma.r

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-gemma.r:<tag>

(see `bioconductor-gemma.r/tags`_ for valid values for ``<tag>``)

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