recipe bioconductor-qsutils

Quasispecies Diversity

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-qsutils/meta.yaml

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.

package bioconductor-qsutils

versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0, 

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-pwalign:

>=1.2.0,<1.3.0

depends r-ape:

depends r-base:

>=4.4,<4.5.0a0

depends r-psych:

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-qsutils

and update with::

   mamba update bioconductor-qsutils

To create a new environment, run:

mamba create --name myenvname bioconductor-qsutils

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-qsutils:<tag>

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

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