recipe bioconductor-lineagespot

Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-lineagespot/meta.yaml

Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

package bioconductor-lineagespot

(downloads) docker_bioconductor-lineagespot

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-httr:

depends r-stringr:

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-lineagespot

and update with::

   mamba update bioconductor-lineagespot

To create a new environment, run:

mamba create --name myenvname bioconductor-lineagespot

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-lineagespot:<tag>

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

Download stats

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/bioconductor-lineagespot/README.html)