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Merged
TuomasBorman merged 1 commit into from
Apr 20, 2026
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Enable Maaslin2 #853

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4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -1,7 +1,7 @@
Package: OMA
Title: Orchestrating Microbiome Analysis with Bioconductor
Version: 0.99.5
Date: 2026-03-26
Version: 0.99.6
Date: 2026-04-20
Authors@R:
c(
person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", comment = c(ORCID = "0000-0002-8563-8884")),
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10 changes: 0 additions & 10 deletions inst/pages/differential_abundance.qmd
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Expand Up @@ -199,11 +199,6 @@ folder for some output files. Lastly, we prevent `Maaslin2()` to create certain
plots. (Note that `Maaslin2()` prints a lot of some output
which is suppressed here for convenience.)

```{r}
#| label: disable_chunks
knitr::opts_chunk$set(eval = FALSE)
```

```{r}
#| label: run_daa_basic
#| results: hide
Expand Down Expand Up @@ -558,11 +553,6 @@ cohort).
Note that a similar plot could also be used to illustrate a possible confounding
effect.

```{r}
#| label: enable_chunks
knitr::opts_chunk$set(eval = TRUE)
```

### Differential prevalence analysis (DPA) {#sec-DPA}

We show here how to perform DPA with logistic regression. We show the case
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7 changes: 0 additions & 7 deletions inst/pages/phyloseq_cheatsheet.qmd
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# phyloseq vs TreeSE cheatsheet {#sec-phyloseq_cheatsheet}

```{r}
#| label: setup
#| echo: false

knitr::opts_chunk$set(eval = TRUE, warning = FALSE, message = FALSE)
```

This section has a cheatsheet for translating common functions in
`r BiocStyle::Biocpkg("phyloseq")` to
`r BiocStyle::Biocpkg("TreeSummarizedExperiment")` (`TreeSE`) /
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