recipe bioconductor-seq.hotspot

Targeted sequencing panel design based on mutation hotspots

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/seq.hotSPOT.html

License:

Artistic-2.0

Recipe:

/bioconductor-seq.hotspot/meta.yaml

seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues.

package bioconductor-seq.hotspot

(downloads) docker_bioconductor-seq.hotspot

versions:

1.6.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-hash:

depends r-r.utils:

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-seq.hotspot

and update with::

   mamba update bioconductor-seq.hotspot

To create a new environment, run:

mamba create --name myenvname bioconductor-seq.hotspot

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-seq.hotspot:<tag>

(see `bioconductor-seq.hotspot/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/bioconductor-seq.hotspot/README.html)