recipe pyseer

Sequence Element Enrichment Analysis (SEER), python implementation

Homepage:

https://github.com/mgalardini/pyseer

License:

APACHE / Apache-2.0

Recipe:

/pyseer/meta.yaml

Links:

doi: 10.1093/bioinformatics/bty539, doi: 10.1101/852426v1

package pyseer

versions:

1.3.12-0,  1.3.11-0,  1.3.10-0,  1.3.9-0,  1.3.8-0,  1.3.7-0,  1.3.6-1,  1.3.6-0,  1.3.5-0, 

1.3.12-0,  1.3.11-0,  1.3.10-0,  1.3.9-0,  1.3.8-0,  1.3.7-0,  1.3.6-1,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-1,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-1,  1.1.0-0,  1.0.2-0,  0.3.1-0

depends bedops:

depends bedtools:

depends bwa:

depends dendropy:

depends glmnet_py:

depends mash:

depends matplotlib-base:

depends numpy:

depends pandas:

depends pybedtools:

depends pysam:

>=0.15.3

depends python:

depends python-dateutil:

>=2.5.0

depends scikit-learn:

depends scipy:

depends statsmodels:

>=0.10

depends tqdm:

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 pyseer

and update with::

   mamba update pyseer

To create a new environment, run:

mamba create --name myenvname pyseer

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/pyseer:<tag>

(see `pyseer/tags`_ for valid values for ``<tag>``)

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