Package Recipe 'bioconductor-seta'

recipe bioconductor-seta

Single Cell Ecological Taxonomic Analysis

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

Tools for compositional and other sample-level ecological analyses and visualizations tailored for single-cell RNA-seq data. SETA includes functions for taxonomizing celltypes, normalizing data, performing statistical tests, and visualizing results. Several tutorials are included to guide users and introduce them to key concepts. SETA is meant to teach users about statistical concepts underlying ecological analysis methods so they can apply them to their own single-cell data.

package bioconductor-seta¶

Versions:

1.0.0-0

Depends:

on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-mass
on r-matrix
on r-rlang
on r-tidygraph

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-seta

to add into an existing workspace instead, run:

pixi add bioconductor-seta

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-seta

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-seta

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-seta:<tag>

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