recipe ls-gkm

gkm-SVM, a sequence-based method for predicting regulatory DNA elements, is a useful tool for studying gene regulatory mechanisms. In continuous efforts to improve the method, new software, LS-GKM, is introduced. It offers much better scalability and provides further advanced gapped k-mer based kernel functions. As a result, LS-GKM achieves considerably higher accuracy than the original gkm-SVM.

Homepage:

https://github.com/Dongwon-Lee/lsgkm

License:

GPL3

Recipe:

/ls-gkm/meta.yaml

package ls-gkm

(downloads) docker_ls-gkm

versions:

0.0.1-1,  0.0.1-0

depends libstdcxx-ng:

>=4.9

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 ls-gkm

and update with::

   mamba update ls-gkm

To create a new environment, run:

mamba create --name myenvname ls-gkm

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/ls-gkm:<tag>

(see `ls-gkm/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda 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/ls-gkm/README.html)