recipe r-bascule

Bayesian inference and clustering of mutational signatures leveraging biological priors

Homepage:

https://github.com/caravagnalab/bascule

Documentation:

https://caravagnalab.github.io/bascule/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/r-bascule/meta.yaml

BASCULE is a Bayesian model to fit multiple signature types from multiple patients, leveraging a pre-existing catalogue of known signatures such as COSMIC. BASCULE searches for known signatures from the input catalogue as well as for new signatures that outside the catalogue, accounting for hidden structure in the input data (e.g., distinct tumour types). Moreover, bascule performs tensor clustering to retrieve latent groups in the input cohort from the exposures of multiple signature types jointly. The model uses non-negative matrix factorisation and variational inference implemented in the pybascule Python package.

package r-bascule

versions:

1.0.1-0,  1.0.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-cli:

depends r-data.table:

depends r-doparallel:

depends r-dplyr:

depends r-ggh4x:

depends r-ggplot2:

depends r-ggplotify:

depends r-ggpubr:

depends r-ggrepel:

depends r-ggsci:

depends r-ggtext:

depends r-gridextra:

depends r-gtools:

depends r-lsa:

depends r-magrittr:

depends r-patchwork:

depends r-pheatmap:

depends r-polychrome:

depends r-progress:

depends r-quadprog:

depends r-reshape2:

depends r-reticulate:

depends r-scales:

depends r-stringr:

depends r-tibble:

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 r-bascule

and update with::

   mamba update r-bascule

To create a new environment, run:

mamba create --name myenvname r-bascule

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-bascule:<tag>

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

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