get_edgeR_results: User friendly interface to edgeR for microbiome data
In audreyrenson/nychanesmicrobiome:

Returns an object of class topTags containing results filtered by FDR < alpha for one comparison. get_edgeR_results_all_levels() returns a list of topTags objects returned by get_edgeR_results() for all levels of the first variable in the formula.

get_edgeR_results(formla, pseq = NYC_HANES, method = c("BH", "IHW"),
  coef = 2, alph = 0.01, filtering = method[1] == "BH",
  countMinimum = 8, percentMinimumHaveCount = NULL, nMinimumHaveCount = 3,
  NA.RM = TRUE)

get_edger_results_all_levels(formla, ...)

`formla`	formula. specifies the design matrix used by `edgeR::glmFit`.
`pseq`	object of class `phyloseq`
`method`	character. Specifies the method of multiple testing correction to apply, either "BH" (Benjamini-Hochberg) or "IHW" (independent hypothesis weighting).
`coef`	integer. Specifies which linear model coefficient to test (default 2).
`alph`	numeric. Specifies what FDR level is considered alpha, and only keeps results with FDR less than this number.
`filtering`	logical. Whether or not to apply pre-filtering.
`countMinimum`	integer. If `filtering==TRUE`, the minimum count required for an OTU to be retained. Requires either `percentMinimumHaveCount` or `nMinimumHaveCount`.
`percentMinimumHaveCount`	numeric. If `filtering==TRUE`, the minimum percentage of samples that must have `countMinimum` counts for an OTU to be retained.
`nMinimumHaveCount`	numeric. If `filtering==TRUE`, the minimum number of samples that must have `countMinimum` counts for an OTU to be retained.
`NA.RM`	logical. Whether or not to remove samples with NA values in the `sample_data()`.
`...`	further arguments passed to `get_edgeR_results`