Package Recipe 'bioconductor-aldex2'

recipe bioconductor-aldex2

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ALDEx2.html
License:: GPL (>=3)
Recipe:: /bioconductor-aldex2/meta.yaml
Links:: biotools: aldex2

A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.

package bioconductor-aldex2¶

Versions:

1.42.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.22.0-0,

1.42.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.14.1-0, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-multtest >=2.66.0,<2.67.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-directlabels
on r-lattice
on r-latticeextra
on r-rfast
on r-zcompositions

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-aldex2

to add into an existing workspace instead, run:

pixi add bioconductor-aldex2

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-aldex2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-aldex2

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-aldex2:<tag>

(see bioconductor-aldex2/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-aldex2/README.html)