recipe bioconductor-hmmcopy

Copy number prediction with correction for GC and mappability bias for HTS data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-hmmcopy/meta.yaml

Links:

biotools: hmmcopy, doi: 10.1038/nmeth.3252

Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.

package bioconductor-hmmcopy

(downloads) docker_bioconductor-hmmcopy

versions:
1.44.0-2,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.36.0-2,  1.36.0-1, 

1.44.0-2,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.36.0-2,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

>=1.11.8

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-hmmcopy

and update with::

   mamba update bioconductor-hmmcopy

To create a new environment, run:

mamba create --name myenvname bioconductor-hmmcopy

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-hmmcopy:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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