From c79cde13ea2d05a9109e850f00242c15dc150e32 Mon Sep 17 00:00:00 2001 From: Tuomas Borman Date: Sun, 15 Mar 2026 12:57:54 +0200 Subject: [PATCH 1/6] Remove extra material --- DESCRIPTION | 50 +------------------ inst/assets/_book.yml | 8 --- inst/pages/{ => extra_material}/extra_daa.qmd | 0 .../integrated_learner.qmd | 0 .../mmuphin_meta_analysis.qmd | 0 inst/pages/{ => extra_material}/msea.qmd | 0 .../network_comparison.qmd | 0 .../{ => extra_material}/network_learning.qmd | 0 8 files changed, 1 insertion(+), 57 deletions(-) rename inst/pages/{ => extra_material}/extra_daa.qmd (100%) rename inst/pages/{ => extra_material}/integrated_learner.qmd (100%) rename inst/pages/{ => extra_material}/mmuphin_meta_analysis.qmd (100%) rename inst/pages/{ => extra_material}/msea.qmd (100%) rename inst/pages/{ => extra_material}/network_comparison.qmd (100%) rename inst/pages/{ => extra_material}/network_learning.qmd (100%) diff --git a/DESCRIPTION b/DESCRIPTION index 04d850ba..2f73859e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,98 +23,50 @@ Depends: R (>= 4.0.0) Imports: Suggests: - ALDEx2, - ANCOMBC, ape, - biclust, BiocBook, BiocManager, - BiocParallel, BiocStyle, - Biostrings, bluster, - caret, - circlize, - cluster, - cobiclust, ComplexHeatmap, - corpcor, - cowplot, curatedMetagenomicData, - dada2, dendextend, - devtools, - DirichletMultinomial, dplyr, DT, factoextra, - fido, - forcats, ggdag, ggExtra, ggplot2, ggpubr, ggtree, - glmnet, glue, - grid, - gsEasy, gt, - gtools, - igraph, - IntegratedLearner, knitr, - limma, - logistf, Maaslin2, maaslin3, mediation, mia, miaTime, miaViz, - microbiome, microbiomeDataSets, - MicrobiomeStat, mikropml, - MMUPHin, MOFA2, - multiview, - NbClust, - NetCoMi, NMF, patchwork, philr, phyloseq, - plotly, - purrr, qgraph, - RColorBrewer, rebook, - reshape2, - reticulate, - rgl, - rms, scales, scater, scuttle, sechm, sessioninfo, shadowtext, - SpiecEasi, - SPRING, stats, - stringr, - SuperLearner, tidySingleCellExperiment, tidyverse, - vegan, - WGCNA, - xgboost -Remotes: - github::stefpeschel/NetCoMi, - github::zdk123/SpiecEasi, - github::GraceYoon/SPRING, - github::himelmallick/IntegratedLearner + vegan VignetteBuilder: knitr RoxygenNote: 7.3.2 BiocType: Book diff --git a/inst/assets/_book.yml b/inst/assets/_book.yml index 7820c347..b77f8962 100644 --- a/inst/assets/_book.yml +++ b/inst/assets/_book.yml @@ -51,15 +51,10 @@ book: - pages/differential_abundance.qmd - pages/correlation.qmd - pages/mediation.qmd - - part: "Networks" - chapters: - - pages/network_learning.qmd - - pages/network_comparison.qmd - part: pages/multiomics.qmd chapters: - pages/cross_correlation.qmd - pages/multiassay_ordination.qmd - - pages/integrated_learner.qmd - part: "Machine learning & statistical modeling" chapters: - pages/machine_learning.qmd @@ -73,9 +68,6 @@ book: - pages/resources.qmd - pages/contributions.qmd appendices: - - pages/msea.qmd - - pages/mmuphin_meta_analysis.qmd - - pages/extra_daa.qmd - pages/phyloseq_cheatsheet.qmd - pages/example_solutions.qmd - pages/session_info.qmd diff --git a/inst/pages/extra_daa.qmd b/inst/pages/extra_material/extra_daa.qmd similarity index 100% rename from inst/pages/extra_daa.qmd rename to inst/pages/extra_material/extra_daa.qmd diff --git a/inst/pages/integrated_learner.qmd b/inst/pages/extra_material/integrated_learner.qmd similarity index 100% rename from inst/pages/integrated_learner.qmd rename to inst/pages/extra_material/integrated_learner.qmd diff --git a/inst/pages/mmuphin_meta_analysis.qmd b/inst/pages/extra_material/mmuphin_meta_analysis.qmd similarity index 100% rename from inst/pages/mmuphin_meta_analysis.qmd rename to inst/pages/extra_material/mmuphin_meta_analysis.qmd diff --git a/inst/pages/msea.qmd b/inst/pages/extra_material/msea.qmd similarity index 100% rename from inst/pages/msea.qmd rename to inst/pages/extra_material/msea.qmd diff --git a/inst/pages/network_comparison.qmd b/inst/pages/extra_material/network_comparison.qmd similarity index 100% rename from inst/pages/network_comparison.qmd rename to inst/pages/extra_material/network_comparison.qmd diff --git a/inst/pages/network_learning.qmd b/inst/pages/extra_material/network_learning.qmd similarity index 100% rename from inst/pages/network_learning.qmd rename to inst/pages/extra_material/network_learning.qmd From f3009785c7dc43786ddf46331237e45703ba7460 Mon Sep 17 00:00:00 2001 From: Tuomas Borman Date: Sun, 15 Mar 2026 13:03:16 +0200 Subject: [PATCH 2/6] Add info on extra material --- inst/index.qmd | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/inst/index.qmd b/inst/index.qmd index a6e12468..d53e67be 100644 --- a/inst/index.qmd +++ b/inst/index.qmd @@ -116,6 +116,15 @@ book. For hands-on practice, the *Training* section provides comprehensive training resources. Finally, *Appendix*, links to further resources and acknowledgments. +::: {.callout-tip icon="true"} + +## Extra material + +See the [**OMA extras**](https://microbiome.github.io/OMA-extras/) site for +additional tutorials and examples! + +::: + ## Building OMA book {#sec-building-oma} This book is automatically built to ensure that all code examples are functional. From 83a3a3ded1e4466162cc99c557a796b61d344978 Mon Sep 17 00:00:00 2001 From: Tuomas Borman Date: Sun, 15 Mar 2026 13:06:40 +0200 Subject: [PATCH 3/6] up --- inst/index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/index.qmd b/inst/index.qmd index d53e67be..729f05f9 100644 --- a/inst/index.qmd +++ b/inst/index.qmd @@ -120,7 +120,7 @@ acknowledgments. ## Extra material -See the [**OMA extras**](https://microbiome.github.io/OMA-extras/) site for +See the [**OMA extras**](https://microbiome.github.io/OMA-extras/) for additional tutorials and examples! ::: From d6f936626dfcef58a657ee86a77b8c66824ac31e Mon Sep 17 00:00:00 2001 From: Tuomas Borman Date: Sun, 15 Mar 2026 13:43:15 +0200 Subject: [PATCH 4/6] bump version --- DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2f73859e..07997028 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: OMA Title: Orchestrating Microbiome Analysis with Bioconductor -Version: 0.98.54 -Date: 2025-09-26 +Version: 0.99.00 +Date: 2026-03-15 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")), @@ -20,7 +20,7 @@ LazyData: true biocViews: Book Depends: - R (>= 4.0.0) + R (>= 4.6.0) Imports: Suggests: ape, From 780e7863fc5a6b20dcc19ea8c80a552cc0b2e85c Mon Sep 17 00:00:00 2001 From: Tuomas Borman Date: Sun, 15 Mar 2026 17:30:50 +0200 Subject: [PATCH 5/6] up --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 07997028..55b0364d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: OMA Title: Orchestrating Microbiome Analysis with Bioconductor -Version: 0.99.00 +Version: 0.99.0 Date: 2026-03-15 Authors@R: c( From 7040827b3f04d07698f96509c3fdae04d1406c3c Mon Sep 17 00:00:00 2001 From: Tuomas Borman Date: Sun, 15 Mar 2026 17:50:56 +0200 Subject: [PATCH 6/6] up --- inst/assets/bibliography.bib | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/inst/assets/bibliography.bib b/inst/assets/bibliography.bib index b7ccf96e..921d256c 100644 --- a/inst/assets/bibliography.bib +++ b/inst/assets/bibliography.bib @@ -584,7 +584,7 @@ @Book{Grolemund2017 @Book{OMA, author = {Tuomas Borman, Leo Lahti and Sudarshan Shetty and Felix M Ernst and others}, title = {Orchestrating Microbiome Analysis with Bioconductor [beta version]}, - year = {2024}, + year = {2026}, url = {microbiome.github.io/oma/} } @@ -1168,10 +1168,10 @@ @Manual{Khlebrodova2021 } @Article {Anwar2025, - author = {Anwar, Ali Mostafa and Jeba, Akewak and Lahti, + author = {Anwar, Ali Mostafa and Jeba, Akewak and Lahti, Leo and Coffey, Eleanor}, - title = {{LimROTS}: A Hybrid Method Integrating Empirical Bayes and - Reproducibility-Optimized Statistics for Robust Analysis of + title = {{LimROTS}: A Hybrid Method Integrating Empirical Bayes and + Reproducibility-Optimized Statistics for Robust Analysis of Proteomics Data}, elocation-id = {2025.02.06.636801}, year = {2025},