recipe bioconductor-decontam

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-decontam/meta.yaml

Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,…). Requires DNA quantitation data or sequenced negative control samples.

package bioconductor-decontam

(downloads) docker_bioconductor-decontam

versions:
1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.1-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

>=2.1.0

depends r-reshape2:

>=1.4.1

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-decontam

and update with::

   mamba update bioconductor-decontam

To create a new environment, run:

mamba create --name myenvname bioconductor-decontam

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-decontam:<tag>

(see `bioconductor-decontam/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-decontam/README.html)