ALDEx tool to examine compositional high-throughput sequence data.
A differential relative count abundance analysis for the comparison of two 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 Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs.
Note on versioning: ALDEx2_2.0.7.2 was the base for adding the package to Bioconductor, and the Bioconductor rules indicate that the initial version must be 0.99.?. Therefore, the current version is ALDEx2_0.99.1.tar.gz. This version contains bug fixes and formatting changes that make it compatible with the Bioconductor rules. This version also has parallel execution turned ##OFF# by default. To enable parallel execution for aldex.clr, aldex.glm and aldex.effect set useMC=TRUE when invoking the functions. This version of ALDEx2 is able to accept a set of custom features for centering all features against. Use ?aldex.clr for more information.
Current version: ALDEx2_1.1.5.tar.gz Current manual: manual/ALDE2_manual.pdf Current vinette: ALDEx2_vignette.pdf
ALDEx 1.0.4 from Fernandes et al, 2013 PLoS ONE for historical reasons.