Package Recipe 'bioconductor-geometrid'

recipe bioconductor-geometrid

A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/geomeTriD.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-geometrid/meta.yaml

The geomeTriD (Three-Dimensional Geometry) Package provides interactive 3D visualization of chromatin structures using the WebGL-based 'three.js' (https://threejs.org/) or the rgl rendering library. It is designed to identify and explore spatial chromatin patterns within genomic regions. The package generates dynamic 3D plots and HTML widgets that integrate seamlessly with Shiny applications, enabling researchers to visualize chromatin organization, detect spatial features, and compare structural dynamics across different conditions and data types.

package bioconductor-geometrid¶

Versions:

1.4.1-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-interactionset >=1.38.0,<1.39.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-trackviewer >=1.46.0,<1.47.0
on r-aricode
on r-base >=4.5,<4.6.0a0
on r-clue
on r-cluster
on r-dbscan
on r-future.apply
on r-htmlwidgets
on r-igraph
on r-mass
on r-matrix
on r-plotrix
on r-progressr
on r-rann
on r-rgl
on r-rjson
on r-scales

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-geometrid

to add into an existing workspace instead, run:

pixi add bioconductor-geometrid

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-geometrid

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-geometrid

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-geometrid:<tag>

(see bioconductor-geometrid/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-geometrid/README.html)