recipe bioconductor-aldex2

Analysis Of Differential Abundance Taking Sample Variation Into Account

Homepage:

https://bioconductor.org/packages/3.16/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 p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.

package bioconductor-aldex2

Versions:

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, 

1.30.0-0,  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:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-multtest >=2.54.0,<2.55.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-rfast

• r-zcompositions

Required By:

• bioconductor-omicplotr

• bioconductor-benchdamic

• bioconductor-microbiomemarker

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-aldex2

and update with:

conda update bioconductor-aldex2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-aldex2:<tag>

(see bioconductor-aldex2/tags for valid values for <tag>)

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