BioConductor

ALDEx2 1.4.0

Analysis of differential abundance taking sample variation into account

Released Jun 27, 2014 by Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links

This package cannot yet be used with Renjin it depends on other packages which are not available: GenomicRanges 1.24.3 and SummarizedExperiment 1.2.3

Dependencies

SummarizedExperiment 1.2.3 GenomicRanges 1.24.3 S4Vectors 0.10.3 IRanges 2.6.1

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.

Source

R

Release History