recipe bioconductor-treeclimbr

An algorithm to find optimal signal levels in a tree

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/treeclimbR.html

License:

Artistic-2.0

Recipe:

/bioconductor-treeclimbr/meta.yaml

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

package bioconductor-treeclimbr

versions:

1.2.0-0

depends bioconductor-diffcyt:

>=1.26.0,<1.27.0

depends bioconductor-edger:

>=4.4.0,<4.5.0

depends bioconductor-ggtree:

>=3.14.0,<3.15.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-treesummarizedexperiment:

>=2.14.0,<2.15.0

depends r-ape:

depends r-base:

>=4.4,<4.5.0a0

depends r-dirmult:

depends r-dplyr:

depends r-ggnewscale:

depends r-ggplot2:

>=3.4.0

depends r-rlang:

depends r-tibble:

depends r-tidyr:

depends r-viridis:

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-treeclimbr

and update with::

   mamba update bioconductor-treeclimbr

To create a new environment, run:

mamba create --name myenvname bioconductor-treeclimbr

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-treeclimbr:<tag>

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

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