recipe r-cnaqc

Copy number quality control

Homepage:

https://github.com/caravagnalab/CNAqc

Documentation:

https://caravagnalab.github.io/CNAqc/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/r-cnaqc/meta.yaml

CNAqc is a package to quality control (QC) bulk cancer sequencing data. Methods are available to , visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. QC procedures in CNAqc can be used to validate copy number segmentations against variant allele frequencies of somatic mutations; QC scores can be used to rank alternative tumour segmentations and purity/ ploidy estimates. CNAqc provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty. The package contains also statistical tests to identify patterns of over-fragmentation of chromosome arms (excessively short and numerous DNA fragments) and perform various manipulation tasks for somatic tumour data.

package r-cnaqc

versions:

1.1.2-0

depends bioconductor-annotationdbi:

depends bioconductor-complexheatmap:

depends bioconductor-genomicranges:

depends bioconductor-rhtslib:

depends bioconductor-rsamtools:

depends bioconductor-variantannotation:

depends r-akima:

depends r-base:

>=4.4,<4.5.0a0

depends r-bmix:

depends r-cli:

depends r-clisymbols:

depends r-cowplot:

depends r-crayon:

depends r-data.table:

depends r-dplyr:

depends r-easypar:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-ggsci:

depends r-gtools:

depends r-magrittr:

depends r-peakpick:

depends r-pio:

depends r-progress:

depends r-r.utils:

depends r-rcolorbrewer:

depends r-readr:

depends r-scales:

depends r-tibble:

depends r-tidyr:

depends r-vcfr:

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-cnaqc

and update with::

   mamba update r-cnaqc

To create a new environment, run:

mamba create --name myenvname r-cnaqc

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-cnaqc:<tag>

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

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