recipe bioconductor-raids

Accurate Inference of Genetic Ancestry from Cancer Sequences

Homepage:

https://bioconductor.org/packages/3.18/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:

1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationfilter:

>=1.26.0,<1.27.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-ensembldb:

>=2.26.0,<2.27.0

depends bioconductor-gdsfmt:

>=1.38.0,<1.39.0

depends bioconductor-genesis:

>=2.32.0,<2.33.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-snprelate:

>=1.36.0,<1.37.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-class:

depends r-proc:

depends r-rlang:

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 bioconductor-raids

and update with::

   mamba update bioconductor-raids

To create a new environment, run:

mamba create --name myenvname bioconductor-raids

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-raids:<tag>

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

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)