- recipe bioconductor-copynumber
Segmentation of single- and multi-track copy number data by penalized least squares regression.
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/copynumber.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: copynumber
Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.
- package bioconductor-copynumber¶
- Versions:
1.38.0-2,1.38.0-1,1.38.0-0,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-0,1.38.0-2,1.38.0-1,1.38.0-0,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.22.0-0,1.20.0-0,1.18.0-0,1.16.0-0- Depends:
on bioconductor-biocgenerics
on bioconductor-genomicranges
1.58.0.*on bioconductor-iranges
on bioconductor-s4vectors
on r-base
>=4.4,<4.5.0a0
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-copynumber
to add into an existing workspace instead, run:
pixi add bioconductor-copynumber
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-copynumber
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-copynumber
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-copynumber:<tag>
(see bioconductor-copynumber/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-copynumber/README.html)
