recipe bioconductor-assessorf

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/AssessORF.html

License:

GPL-3

Recipe:

/bioconductor-assessorf/meta.yaml

In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence.

package bioconductor-assessorf

versions:

1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1, 

1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.2-0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-decipher:

>=2.28.0,<2.29.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends r-base:

>=4.3,<4.4.0a0

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-assessorf

and update with::

   mamba update bioconductor-assessorf

To create a new environment, run:

mamba create --name myenvname bioconductor-assessorf

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-assessorf:<tag>

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

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