ALDEx2
Bioc currentAnalysis Of Differential Abundance Taking Sample and Scale Variation Into Account
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
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.
Code & tests
Open call graph →Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 3 exported
Complexity
9.5 avg / 48 max
Call network
31 nodes / 26 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
12,381
Files
87
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
14
Testing & CI
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>=3)
License flags
not SPDX, not OSI
History
Versions
24
First release
2014-10-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Topics
Depended on by (8)
Bioconductor (4)
CRAN (4)
People
Greg Gloor