recipe r-biomartr

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', 'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

Homepage:

https://docs.ropensci.org/biomartr, https://github.com/ropensci/biomartr

License:

GPL2 / GPL-2.0-only

Recipe:

/r-biomartr/meta.yaml

package r-biomartr

versions:

1.0.7-1,  1.0.7-0,  1.0.6-1,  1.0.6-0,  1.0.4-1,  1.0.4-0,  1.0.3-0,  1.0.2-1,  1.0.2-0, 

1.0.7-1,  1.0.7-0,  1.0.6-1,  1.0.6-0,  1.0.4-1,  1.0.4-0,  1.0.3-0,  1.0.2-1,  1.0.2-0,  0.9.2-2,  0.9.2-1,  0.9.2-0

depends bioconductor-biomart:

depends bioconductor-biostrings:

depends r-base:

>=4.3,<4.4.0a0

depends r-curl:

depends r-data.table:

>=1.9.4

depends r-downloader:

>=0.3

depends r-dplyr:

>=0.3.0

depends r-fs:

depends r-httr:

>=0.6.1

depends r-jsonlite:

depends r-philentropy:

depends r-purrr:

depends r-r.utils:

depends r-rcurl:

>=1.95_4.5

depends r-readr:

>=1.4.0

depends r-stringr:

>=0.6.2

depends r-tibble:

depends r-withr:

depends r-xml:

>=3.98_1.1

requirements:

additional platforms:

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 r-biomartr

and update with::

   mamba update r-biomartr

To create a new environment, run:

mamba create --name myenvname r-biomartr

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/r-biomartr:<tag>

(see `r-biomartr/tags`_ for valid values for ``<tag>``)

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