Package: ALDEx2
Type: Package
Title: Analysis Of Differential Abundance Taking Sample Variation Into
        Account
Version: 1.32.0
Date: 2022-05-09
Author: Greg Gloor, Andrew Fernandes, Jean Macklaim, Arianne Albert, Matt Links,
    Thomas Quinn, Jia Rong Wu, Ruth Grace Wong, Brandon Lieng
Maintainer: Greg Gloor <ggloor@uwo.ca>
biocViews: DifferentialExpression, RNASeq, Transcriptomics,
        GeneExpression, DNASeq, ChIPSeq, Bayesian, Sequencing,
        Software, Microbiome, Metagenomics, ImmunoOncology
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 p-values and Benjamini-Hochberg
    corrected p-values. ALDEx2 also calculates expected standardized effect sizes for
    paired or unpaired study designs.
License: GPL (>= 3)
URL: https://github.com/ggloor/ALDEx_bioc
BugReports: https://github.com/ggloor/ALDEx_bioc/issues
RoxygenNote: 7.2.0
VignetteBuilder: knitr
Depends: methods, stats, zCompositions,
Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors,
        SummarizedExperiment, multtest
Suggests: testthat, BiocStyle, knitr, rmarkdown
git_url: https://git.bioconductor.org/packages/ALDEx2
git_branch: RELEASE_3_17
git_last_commit: ba32b9a
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-25 20:10:23 UTC; biocbuild
Built: R 4.3.0; ; 2023-07-11 18:11:48 UTC; unix
