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qiime2 composition ancombc2 (version 2025.7.0+q2galaxy.2025.7.0)
[required] The feature table to be used for ANCOM-BC2 computation.
metadata: Metadatas
metadata: Metadata 0
[required] A formula that expresses how the feature absolute abundances in the feature table depend on the fixed effects of variables (columns) in the metadata. Do not include the dependent variable. Reference the `formula` function in the `stats` R package for a specification of valid formulae.
Click here for additional options
Click here for additional options 0

QIIME 2: composition ancombc2

ANCOM-BC2: Analysis of Composition of Microbiomes with Bias Correction 2.

Outputs:

ancombc2_output.qza:
 The estimated log fold changes and their standard errors for the variables included in the mixed effects model. Also includes the structural zero designations if the structural_zeros parameter is passed.

Description:

Calls the ancombc2 function of the ANCOMBC software package. See the ANCOM-BC2 publication and source code for details.

Examples:

single-variable

Using the qiime2 composition ancombc2 tool:
  1. Set "table" to #: table.qza
  2. For "metadata":
    • Perform the following steps.
      1. Leave as Metadata from TSV
      2. Set "Metadata Source" to metadata.tsv
  3. Set "fixed_effects_formula" to bodysite
  4. Press the Execute button.
Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name "Name" to set (be sure to press Save)
#: qiime2 composition ancombc2 [...] : ancombc2_output.qza abc2-output.qza

multi-variable-reference

Using the qiime2 composition ancombc2 tool:
  1. Set "table" to #: table.qza
  2. For "metadata":
    • Perform the following steps.
      1. Leave as Metadata from TSV
      2. Set "Metadata Source" to metadata.tsv
  3. Set "fixed_effects_formula" to bodysite + animal
  4. Expand the additional options section
    • For "reference_levels", use the + reference_levels button to add the corresponding values:
      1. Add "element" set to bodysite::tongue
      2. Add "element" set to animal::dog
  5. Press the Execute button.
Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name "Name" to set (be sure to press Save)
#: qiime2 composition ancombc2 [...] : ancombc2_output.qza abc2-output.qza