recipe bioconductor-traviz

Trajectory functions for visualization and interpretation.

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/traviz.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-traviz/meta.yaml

traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.

package bioconductor-traviz

versions:

1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-singlecellexperiment:

>=1.22.0,<1.23.0

depends bioconductor-slingshot:

>=2.8.0,<2.9.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-mgcv:

depends r-princurve:

depends r-rcolorbrewer:

depends r-rgl:

depends r-viridis:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-traviz

and update with::

   mamba update bioconductor-traviz

To create a new environment, run:

mamba create --name myenvname bioconductor-traviz

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-traviz:<tag>

(see `bioconductor-traviz/tags`_ for valid values for ``<tag>``)

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-traviz/README.html)