- recipe bioconductor-epidish
Epigenetic Dissection of Intra-Sample-Heterogeneity
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/EpiDISH.html
- License:
GPL-2
- Recipe:
EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.
- package bioconductor-epidish¶
- Versions:
2.26.0-0,2.22.0-0,2.18.0-0,2.16.0-0,2.14.0-0,2.10.0-0,2.8.0-0,2.6.0-1,2.6.0-0,2.26.0-0,2.22.0-0,2.18.0-0,2.16.0-0,2.14.0-0,2.10.0-0,2.8.0-0,2.6.0-1,2.6.0-0,2.4.0-0,2.2.0-0,2.0.2-1,2.0.2-0,1.4.1-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-e1071
on r-locfdr
on r-mass
on r-matrix
on r-matrixstats
on r-quadprog
on r-stringr
- 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-epidish
to add into an existing workspace instead, run:
pixi add bioconductor-epidish
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-epidish
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-epidish
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-epidish:<tag>
(see bioconductor-epidish/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-epidish/README.html)
