- recipe bioconductor-massarray
Analytical Tools for MassArray Data
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/MassArray.html
- License:
GPL (>=2)
- Recipe:
- Links:
biotools: massarray, doi: 10.1093/bioinformatics/btp382
This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.
- package bioconductor-massarray¶
- Versions:
1.62.0-0,1.58.0-0,1.54.0-1,1.54.0-0,1.52.0-0,1.50.0-0,1.46.0-0,1.44.0-0,1.42.0-1,1.62.0-0,1.58.0-0,1.54.0-1,1.54.0-0,1.52.0-0,1.50.0-0,1.46.0-0,1.44.0-0,1.42.0-1,1.42.0-0,1.40.0-0,1.38.0-0,1.36.0-1,1.36.0-0,1.34.1-0,1.32.0-0,1.30.0-0,1.28.0-0- Depends:
on r-base
>=4.5,<4.6.0a0
- 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-massarray
to add into an existing workspace instead, run:
pixi add bioconductor-massarray
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-massarray
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-massarray
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-massarray:<tag>
(see bioconductor-massarray/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-massarray/README.html)
