:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'liquorice' .. highlight: bash liquorice ========= .. conda:recipe:: liquorice :replaces_section_title: :noindex: A tool for bias correction and quantification of changes in coverage around regions of interest in cfDNA WGS datasets :homepage: https://github.com/epigen/LIQUORICE :license: GPL / GPL-3.0 :recipe: /`liquorice `_/`meta.yaml `_ See https\:\/\/liquorice.readthedocs.io for more information. .. conda:package:: liquorice |downloads_liquorice| |docker_liquorice| :versions: ``0.5.6-0``,  ``0.5.5-1``,  ``0.5.5-0``,  ``0.5.4-0``,  ``0.5.3-0`` :depends biopython: ``1.79`` :depends deeptools: ``3.5.1`` :depends joblib: ``1.0.1`` :depends lmfit: ``1.0.2`` :depends matplotlib-base: ``3.1.1`` :depends modin: ``0.8.2`` :depends numpy: ``1.21.2`` :depends pandas: ``1.1.4`` :depends parallel: :depends pybedtools: ``0.8.2`` :depends pybigwig: ``0.3.18`` :depends pysam: ``0.16.0.1`` :depends python: ``>=3.7.9`` :depends scikit-learn: ``0.24.2`` :depends scipy: ``1.7.1`` :depends seaborn: ``0.11.2`` :depends swifter: ``1.0.9`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 liquorice and update with:: mamba update liquorice To create a new environment, run:: mamba create --name myenvname liquorice 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/liquorice: (see `liquorice/tags`_ for valid values for ````) .. |downloads_liquorice| image:: https://img.shields.io/conda/dn/bioconda/liquorice.svg?style=flat :target: https://anaconda.org/bioconda/liquorice :alt: (downloads) .. |docker_liquorice| image:: https://quay.io/repository/biocontainers/liquorice/status :target: https://quay.io/repository/biocontainers/liquorice .. _`liquorice/tags`: https://quay.io/repository/biocontainers/liquorice?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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/liquorice/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/liquorice/README.html