recipe bioconductor-sarc

Statistical Analysis of Regions with CNVs

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SARC.html

License:

GPL-3

Recipe:

/bioconductor-sarc/meta.yaml

Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.

package bioconductor-sarc

versions:

1.0.0-0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-multtest:

>=2.58.0,<2.59.0

depends bioconductor-plyranges:

>=1.22.0,<1.23.0

depends bioconductor-raggedexperiment:

>=1.26.0,<1.27.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-desctools:

depends r-ggplot2:

depends r-gridextra:

depends r-gtable:

depends r-metap:

depends r-plotly:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scales:

depends r-tidyverse:

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-sarc

and update with::

   mamba update bioconductor-sarc

To create a new environment, run:

mamba create --name myenvname bioconductor-sarc

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-sarc:<tag>

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

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