- recipe r-bascule
Bayesian inference and clustering of mutational signatures leveraging biological priors
- Homepage:
- Documentation:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
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:
on r-base
>=4.4,<4.5.0a0on r-cli
on r-data.table
on r-doparallel
on r-dplyr
on r-ggh4x
on r-ggplot2
on r-ggplotify
on r-ggpubr
on r-ggrepel
on r-ggsci
on r-ggtext
on r-gridextra
on r-gtools
on r-lsa
on r-magrittr
on r-patchwork
on r-pheatmap
on r-polychrome
on r-progress
on r-quadprog
on r-reshape2
on r-reticulate
on r-scales
on r-stringr
on r-tibble
on r-tidyr
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install r-bascule
to add into an existing workspace instead, run:
pixi add r-bascule
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install r-bascule
Alternatively, to install into a new environment, run:
conda create -n envname r-bascule
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/r-bascule:<tag>
(see r-bascule/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/r-bascule/README.html)
