Package Recipe 'bioconductor-raids'

recipe bioconductor-raids

Accurate Inference of Genetic Ancestry from Cancer Sequences

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/RAIDS.html
License:: Apache License (>= 2)
Recipe:: /bioconductor-raids/meta.yaml

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

package bioconductor-raids¶

Versions:

1.8.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationfilter >=1.34.0,<1.35.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-ensembldb >=2.34.0,<2.35.0
on bioconductor-gdsfmt >=1.46.0,<1.47.0
on bioconductor-genesis >=2.40.0,<2.41.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-snprelate >=1.44.0,<1.45.0
on bioconductor-variantannotation >=1.56.0,<1.57.0
on r-base >=4.5,<4.6.0a0
on r-class
on r-dplyr
on r-ggplot2
on r-proc
on r-rlang
on r-stringr

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 bioconductor-raids

to add into an existing workspace instead, run:

pixi add bioconductor-raids

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 bioconductor-raids

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-raids

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/bioconductor-raids:<tag>

(see bioconductor-raids/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-raids/README.html)