ALDEx2: Analysis Of Differential Abundance Taking Sample Variation Into Account

A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.

AuthorGreg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links, Jia Rong Wu
Date of publicationNone
MaintainerGreg Gloor <ggloor@uwo.ca>
Licensefile LICENSE
Version1.6.0

View on Bioconductor

Functions

aldex Man page
ALDEx2m Man page
ALDEx2m-package Man page
aldex.clr Man page
aldex.clr-class Man page
aldex.clr,data.frame-method Man page
aldex.clr.function Man page
aldex.clr,RangedSummarizedExperiment-method Man page
aldex.corr Man page
aldex.effect Man page
aldex.glm Man page
aldex.plot Man page
aldex.set.mode Man page
aldex.ttest Man page
getFeatureNames Man page
getFeatureNames,aldex.clr-method Man page
getFeatures Man page
getFeatures,aldex.clr-method Man page
getMonteCarloInstances Man page
getMonteCarloInstances,aldex.clr-method Man page
getMonteCarloReplicate Man page
getMonteCarloReplicate,aldex.clr,numeric-method Man page
getReads Man page
getReads,aldex.clr-method Man page
getSampleIDs Man page
getSampleIDs,aldex.clr-method Man page
numConditions Man page
numConditions,aldex.clr-method Man page
numFeatures Man page
numFeatures,aldex.clr-method Man page
numMCInstances Man page
numMCInstances,aldex.clr-method Man page
selex Man page

Files

ALDEx2/DESCRIPTION
ALDEx2/LICENSE
ALDEx2/NAMESPACE
ALDEx2/NEWS
ALDEx2/R
ALDEx2/R/AllClasses.R ALDEx2/R/AllGenerics.R
ALDEx2/R/aldex.r
ALDEx2/R/clr_corr.R
ALDEx2/R/clr_effect.r
ALDEx2/R/clr_function.r
ALDEx2/R/clr_glm.r
ALDEx2/R/clr_ttest.r
ALDEx2/R/iqlr_features.r
ALDEx2/R/plot.aldex.r
ALDEx2/R/rdirichlet.r
ALDEx2/build
ALDEx2/build/vignette.rds
ALDEx2/data
ALDEx2/data/selex.txt.gz
ALDEx2/inst
ALDEx2/inst/CITATION
ALDEx2/inst/doc
ALDEx2/inst/doc/ALDEx2_vignette.R
ALDEx2/inst/doc/ALDEx2_vignette.Rnw
ALDEx2/inst/doc/ALDEx2_vignette.pdf
ALDEx2/man
ALDEx2/man/ALDEx2m-package.Rd ALDEx2/man/aldex.Rd ALDEx2/man/aldex.clr-class.Rd ALDEx2/man/aldex.clr.function-methods.Rd ALDEx2/man/aldex.corr.Rd ALDEx2/man/aldex.effect.Rd ALDEx2/man/aldex.glm.Rd ALDEx2/man/aldex.set.mode.Rd ALDEx2/man/aldex.ttest.Rd ALDEx2/man/getFeatureNames-method.Rd ALDEx2/man/getFeatures-method.Rd ALDEx2/man/getMonteCarloInstances-method.Rd ALDEx2/man/getMonteCarloReplicate-method.Rd ALDEx2/man/getReads-method.Rd ALDEx2/man/getSampleIDs-method.Rd ALDEx2/man/numConditions-method.Rd ALDEx2/man/numFeatures-method.Rd ALDEx2/man/numMCInstances-method.Rd ALDEx2/man/plot.aldex.Rd ALDEx2/man/selex.Rd
ALDEx2/vignettes
ALDEx2/vignettes/ALDEx2_vignette.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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