recipe r-dowser

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2020) <doi:10.1101/2020.05.30.124446>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Homepage:

https://dowser.readthedocs.io

License:

AGPL / AGPL-3

Recipe:

/r-dowser/meta.yaml

package r-dowser

versions:

1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.0-0,  0.1.0-0

depends bioconductor-biostrings:

depends bioconductor-ggtree:

depends r-alakazam:

>=1.1.0

depends r-ape:

>=5.5

depends r-base:

>=4.2,<4.3.0a0

depends r-dplyr:

>=0.8.1

depends r-ggplot2:

>=3.2.0

depends r-gridextra:

depends r-markdown:

depends r-phangorn:

>=2.7.1

depends r-phylotate:

depends r-rcolorbrewer:

depends r-rlang:

depends r-shazam:

>=1.1.0

depends r-stringr:

depends r-tidyr:

depends r-tidyselect:

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 r-dowser

and update with::

   mamba update r-dowser

To create a new environment, run:

mamba create --name myenvname r-dowser

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/r-dowser:<tag>

(see `r-dowser/tags`_ for valid values for ``<tag>``)

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