Package Recipe 'bioconductor-pedixplorer'

recipe bioconductor-pedixplorer

Pedigree Functions

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/Pedixplorer.html
License:: Artistic-2.0
Recipe:: /bioconductor-pedixplorer/meta.yaml

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

package bioconductor-pedixplorer¶

Versions:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-base >=4.5,<4.6.0a0
on r-colourpicker
on r-dplyr
on r-dt
on r-ggplot2
on r-htmlwidgets
on r-igraph
on r-matrix
on r-plotly
on r-plyr
on r-quadprog
on r-readxl
on r-shiny
on r-shinycssloaders
on r-shinyhelper
on r-shinyjqui
on r-shinyjs
on r-shinytoastr
on r-shinywidgets
on r-stringr
on r-tidyr

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-pedixplorer

to add into an existing workspace instead, run:

pixi add bioconductor-pedixplorer

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-pedixplorer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pedixplorer

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-pedixplorer:<tag>

(see bioconductor-pedixplorer/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-pedixplorer/README.html)