Package Recipe 'bioconductor-anaquin'

recipe bioconductor-anaquin

Statistical analysis of sequins

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/Anaquin.html
License:: BSD_3_clause + file LICENSE
Recipe:: /bioconductor-anaquin/meta.yaml

The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.

package bioconductor-anaquin¶

Versions:

2.34.0-0, 2.30.0-0, 2.26.0-0, 2.24.0-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.14.0-0,

2.34.0-0, 2.30.0-0, 2.26.0-0, 2.24.0-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.14.0-0, 2.12.0-0, 2.10.0-0, 2.8.0-1, 2.6.0-0

Depends:

on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-qvalue >=2.42.0,<2.43.0
on r-base >=4.5,<4.6.0a0
on r-ggplot2 >=2.2.0
on r-knitr
on r-locfit
on r-plyr
on r-rocr

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-anaquin

to add into an existing workspace instead, run:

pixi add bioconductor-anaquin

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-anaquin

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-anaquin

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-anaquin:<tag>

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