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Bioconductor failure and risk of deprecation

Status: Open.

#1796 In joey711/phyloseq;

· lshep opened on Jan 6, 2026

query about rarefy_even_depth

Status: Open.

#1795 In joey711/phyloseq;

· we32i225 opened on Dec 1, 2025

aes_string()` deprecated

Status: Open.

#1794 In joey711/phyloseq;

· Masoleno opened on Oct 31, 2025

Create .fasta file for tree generation from phyloseq object or dataframe

Status: Open.

#1793 In joey711/phyloseq;

· billstudabaker opened on Oct 27, 2025

Mothur taxonomy data will not import

Status: Open.

#1792 In joey711/phyloseq;

· JSPinelo opened on Oct 23, 2025

phyloseq installation problem

Status: Open.

#1791 In joey711/phyloseq;

· Mewgia opened on Oct 20, 2025

Merging phyloseqs drops taxa lacking refseq -- if one object has refseq, only those taxa will be included

Status: Open.

#1790 In joey711/phyloseq;

· nickp60 opened on Sep 12, 2025

filtering issue

Status: Open.

#1789 In joey711/phyloseq;

· nibaskumar93n-debug opened on Aug 29, 2025

why is it that when searching for a taxa as a factor i get something different than when it is a character?

Status: Open.

#1788 In joey711/phyloseq;

· gabrielet opened on Aug 15, 2025

Use of rarefy_even_depth() for repeated subsampling (empirical rarefaction)

Status: Open.

#1787 In joey711/phyloseq;

· SalmaSarker opened on Aug 5, 2025

Error message when creating a phyloseq object

Status: Open.

#1786 In joey711/phyloseq;

· hammerklaviersonate opened on Jul 19, 2025

Extract and quantify the relative abundance of AOA, AOB and comammox candidates

Status: Open.

#1785 In joey711/phyloseq;

· ksweta596 opened on Jun 1, 2025