recipe bioconductor-dnabarcodes

A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-dnabarcodes/meta.yaml

Links:

biotools: dnabarcodes

The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.

package bioconductor-dnabarcodes

versions:

1.36.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-2,  1.28.0-1,  1.28.0-0,  1.24.0-2,  1.24.0-1, 

1.36.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-2,  1.28.0-1,  1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-bh:

depends r-matrix:

depends r-rcpp:

>=0.11.2

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-dnabarcodes

and update with::

   mamba update bioconductor-dnabarcodes

To create a new environment, run:

mamba create --name myenvname bioconductor-dnabarcodes

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-dnabarcodes:<tag>

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

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