recipe bioconductor-missrows

Handling Missing Individuals in Multi-Omics Data Integration

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/missRows.html

License:

Artistic-2.0

Recipe:

/bioconductor-missrows/meta.yaml

The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.

package bioconductor-missrows

(downloads) docker_bioconductor-missrows

Versions:
1.30.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0, 

1.30.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends:

  • on bioconductor-multiassayexperiment >=1.36.0,<1.37.0

  • on bioconductor-s4vectors >=0.48.0,<0.49.0

  • on r-base >=4.5,<4.6.0a0

  • on r-ggplot2

  • on r-gtools

  • on r-plyr

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-missrows

to add into an existing workspace instead, run:

pixi add bioconductor-missrows

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-missrows

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-missrows

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-missrows:<tag>

(see bioconductor-missrows/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 install-with-bioconda 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-missrows/README.html)