recipe bioconductor-dnabarcodecompatibility

A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-dnabarcodecompatibility/meta.yaml

The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage.

package bioconductor-dnabarcodecompatibility

versions:

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0, 

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.2-0

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-dplyr:

depends r-numbers:

depends r-purrr:

depends r-rcpp:

>=0.11.2

depends r-stringr:

depends r-tidyr:

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-dnabarcodecompatibility

and update with::

   mamba update bioconductor-dnabarcodecompatibility

To create a new environment, run:

mamba create --name myenvname bioconductor-dnabarcodecompatibility

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-dnabarcodecompatibility:<tag>

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

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