recipe bioconductor-trajectorygeometry

This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-trajectorygeometry/meta.yaml

Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.

package bioconductor-trajectorygeometry

(downloads) docker_bioconductor-trajectorygeometry

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-pracma:

depends r-rgl:

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-trajectorygeometry

and update with::

   mamba update bioconductor-trajectorygeometry

To create a new environment, run:

mamba create --name myenvname bioconductor-trajectorygeometry

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-trajectorygeometry:<tag>

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

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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-trajectorygeometry/README.html)