recipe bioconductor-seqbias

Estimation of per-position bias in high-throughput sequencing data

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-seqbias/meta.yaml

This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

package bioconductor-seqbias

versions:

1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-1, 

1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.30.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0a0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

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-seqbias

and update with::

   mamba update bioconductor-seqbias

To create a new environment, run:

mamba create --name myenvname bioconductor-seqbias

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-seqbias:<tag>

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

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