- 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:
- 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
- Required By:
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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-aldex2/README.html)