- recipe r-eacon
Easy Copy Number. EaCoN aims to be an all-packed in, user-friendly solution to perform relative or absolute copy-number analysis for multiple sources of data, with three different segmenters available (and corresponding three copy-number modelization methods)
- Homepage:
- License:
MIT
- Recipe:
- package r-eacon¶
- Versions:
0.3.6-2,0.3.6-1,0.3.6-0,0.3.5-1,0.3.5-0,0.3.4_1-1,0.3.4_1-0- Depends:
on ascat
>=3on bioconductor-affxparser
on bioconductor-aroma.light
on bioconductor-biostrings
on bioconductor-bsgenome.hsapiens.1000genomes.hs37d5
on bioconductor-copynumber
on bioconductor-genomicranges
on bioconductor-limma
on bioconductor-rhdf5
on bioconductor-rsamtools
on r-base
>=4.2,<4.3.0a0on r-bedr
on r-changepoint
on r-data.table
on r-doparallel
on r-dplyr
on r-dt
on r-facets
on r-foreach
on r-iotools
on r-mclust
on r-rmarkdown
on r-seqinr
on r-sequenza
- 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 r-eacon
to add into an existing workspace instead, run:
pixi add r-eacon
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 r-eacon
Alternatively, to install into a new environment, run:
conda create -n envname r-eacon
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/r-eacon:<tag>
(see r-eacon/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/r-eacon/README.html)
