recipe bioconductor-single

Accurate consensus sequence from nanopore reads of a gene library

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-single/meta.yaml

Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant. More information in preprint doi: https://doi.org/10.1101/2020.03.25.007146.

package bioconductor-single

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-reshape2:

depends r-rlang:

depends r-stringr:

depends r-tidyr:

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-single

and update with::

   mamba update bioconductor-single

To create a new environment, run:

mamba create --name myenvname bioconductor-single

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-single:<tag>

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

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