Package Recipe 'bioconductor-rfpred'

recipe bioconductor-rfpred

Assign rfPred functional prediction scores to a missense variants list

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/rfPred.html
License:: GPL (>=2 )
Recipe:: /bioconductor-rfpred/meta.yaml
Links:: biotools: rfpred, doi: 10.1101/037127

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).

package bioconductor-rfpred¶

Versions:

1.48.0-0, 1.44.0-1, 1.44.0-0, 1.40.0-0, 1.38.0-0, 1.36.0-1, 1.36.0-0, 1.32.0-2, 1.32.0-1,

1.48.0-0, 1.44.0-1, 1.44.0-0, 1.40.0-0, 1.38.0-0, 1.36.0-1, 1.36.0-0, 1.32.0-2, 1.32.0-1, 1.32.0-0, 1.30.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0

Depends:

on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-data.table

Additional platforms:

linux-aarch64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-rfpred

to add into an existing workspace instead, run:

pixi add bioconductor-rfpred

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-rfpred

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rfpred

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-rfpred:<tag>

(see bioconductor-rfpred/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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-rfpred/README.html)