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convertToPhyloseq: row order is different between input TreeSE and output phyloseq

Status: Open.

#821 In microbiome/mia;

· RiboRings opened on Apr 14, 2026

getDominance?

Status: Open.

#819 In microbiome/mia;

· antagomir opened on Apr 10, 2026

rbiom class not supported

Status: Open.

#818 In microbiome/mia;

· RiboRings opened on Apr 10, 2026

deprecation warnings from scuttle::sumCountsAcrossFeatures

Status: Open.

#817 In microbiome/mia;

· lwaldron opened on Apr 9, 2026

agglomerateByPrevalence name is misleading?

Status: Open.

#816 In microbiome/mia;

· antagomir opened on Apr 9, 2026

Transformations non consistent

Status: Open.

#813 In microbiome/mia;

· antagomir opened on Mar 23, 2026

Implement ENBI

Status: Open.

#807 In microbiome/mia;

· antagomir opened on Mar 2, 2026

Simplify examples

Status: Open.

#806 In microbiome/mia;

· antagomir opened on Mar 1, 2026

Polish robust PCA

Status: Open.

#805 In microbiome/mia;

· TuomasBorman opened on Feb 25, 2026

verbose argument for transformAssay (.apply_pseudocount) (and maybe other functions?)

Status: Open.

#788 In microbiome/mia;

· nr0cinu opened on Oct 22, 2025

Clarification: getDissimilarity overlap metric appears to measure similarity

Status: Open.

#787 In microbiome/mia;

· ShivangPB opened on Oct 22, 2025

ecodive: A new, dependency-free package for diversity metrics (from rbiom dev)

Status: Open.

#783 In microbiome/mia;

· dansmith01 opened on Sep 23, 2025