- 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:
- 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¶
- 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:
- additional platforms:
linux-aarch64
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>``)
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-hmmcopy/README.html)