recipe bioconductor-odseq

Outlier detection in multiple sequence alignments

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-odseq/meta.yaml

Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences.

package bioconductor-odseq

versions:

1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0, 

1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0

depends bioconductor-kebabs:

>=1.40.0,<1.41.0

depends bioconductor-msa:

>=1.38.0,<1.39.0

depends r-base:

>=4.4,<4.5.0a0

depends r-mclust:

>=5.1

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 bioconductor-odseq

and update with::

   mamba update bioconductor-odseq

To create a new environment, run:

mamba create --name myenvname bioconductor-odseq

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-odseq:<tag>

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

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