Remove extra material

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OMA
 Title: Orchestrating Microbiome Analysis with Bioconductor
-Version: 0.98.54
-Date: 2025-09-26
+Version: 0.99.0
+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")),
@@ -20,101 +20,53 @@ LazyData: true
 biocViews:
     Book
 Depends:
-    R (>= 4.0.0)
+    R (>= 4.6.0)
 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

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

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},

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/) for
+additional tutorials and examples!
+
+:::
+
 ## Building OMA book {#sec-building-oma}
 
 This book is automatically built to ensure that all code examples are functional.