galaxyproject · lenaarenot · May 14, 2024 · May 14, 2024 · May 22, 2024 · May 24, 2024
diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -1211,6 +1211,10 @@ LeilyR:
     name: Leily Rabbani
     joined: 2018-09
 
+lenaarenot:
+    name: Lena Arent
+    joined: 2024-05
+
 abueg:
     name: Linelle Abueg
     joined: 2022-01

diff --git a/topics/microbiome/tutorials/visualisation-ampvis/data-library.yaml b/topics/microbiome/tutorials/visualisation-ampvis/data-library.yaml
@@ -0,0 +1,39 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Metagenomics
+  description: Training material for visualisation methods on amplicon data with ampvis2
+  items:
+  - name: Divers and Adaptable Visualisations of Metabarcoding Data Using ampvis2
+    items:
+    - name: 'DOI: 10.5281/zenodo.12591715'
+      description: latest
+      items:
+      - url: MiDAS_otushort_table.tsv
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12591715
+      - url: MiDAS_metadata.tsv
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12591715
+      - url: MiDAS_taxtable.tsv
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12591715
+    - name: 'DOI: 10.5281/zenodo.10362755'
+      items:
+      - url: BIOMARCS_ASV_tables.xlsx
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/10362755
+    - name: 'DOI: 10.5281/zenodo.7020318'
+      items:
+      - url: closed_otu_table_mc2_w_tax_0.00005_rarefied12000_filtered.biom
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/7020318
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/faqs/index.md b/topics/microbiome/tutorials/visualisation-ampvis/faqs/index.md
@@ -0,0 +1,5 @@
+---
+layout: faq-page
+redirect_from:
+- /topics/metagenomics/tutorials/visualisation-ampvis/faqs/index
+---
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/all_data.png b/topics/microbiome/tutorials/visualisation-ampvis/images/all_data.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/boxplot_other.png b/topics/microbiome/tutorials/visualisation-ampvis/images/boxplot_other.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/boxplot_period.png b/topics/microbiome/tutorials/visualisation-ampvis/images/boxplot_period.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/choose_parameters.png b/topics/microbiome/tutorials/visualisation-ampvis/images/choose_parameters.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_gr_by_plant.png b/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_gr_by_plant.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_gr_by_year.png b/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_gr_by_year.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_no_group.png b/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_no_group.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_plant_period.png b/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_plant_period.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_year_period.png b/topics/microbiome/tutorials/visualisation-ampvis/images/heatmap_year_period.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/meta.png b/topics/microbiome/tutorials/visualisation-ampvis/images/meta.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/meta_row.png b/topics/microbiome/tutorials/visualisation-ampvis/images/meta_row.png
diff --git a/...s/microbiome/tutorials/visualisation-ampvis/images/ordination_cca_hellinger.png b/...s/microbiome/tutorials/visualisation-ampvis/images/ordination_cca_hellinger.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/ordination_pca.png b/topics/microbiome/tutorials/visualisation-ampvis/images/ordination_pca.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/ordination_pca_date.png b/topics/microbiome/tutorials/visualisation-ampvis/images/ordination_pca_date.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/otu.png b/topics/microbiome/tutorials/visualisation-ampvis/images/otu.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/overview.png b/topics/microbiome/tutorials/visualisation-ampvis/images/overview.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/overview.png:Zone.Identifier b/topics/microbiome/tutorials/visualisation-ampvis/images/overview.png:Zone.Identifier
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/rarefaction.png b/topics/microbiome/tutorials/visualisation-ampvis/images/rarefaction.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/rarefaction_without.png b/topics/microbiome/tutorials/visualisation-ampvis/images/rarefaction_without.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/taxa.png b/topics/microbiome/tutorials/visualisation-ampvis/images/taxa.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/timeseries.png b/topics/microbiome/tutorials/visualisation-ampvis/images/timeseries.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/images/upload_biom.png b/topics/microbiome/tutorials/visualisation-ampvis/images/upload_biom.png
diff --git a/topics/microbiome/tutorials/visualisation-ampvis/tutorial.bib b/topics/microbiome/tutorials/visualisation-ampvis/tutorial.bib
@@ -0,0 +1,62 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Andersen2018,
+  title = {ampvis2: an R package to analyse and visualise 16S rRNA amplicon data},
+  url = {http://dx.doi.org/10.1101/299537},
+  DOI = {10.1101/299537},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Andersen,  Kasper S. and Kirkegaard,  Rasmus H. and Karst,  Søren M. and Albertsen,  Mads},
+  year = {2018},
+  month = apr 
+}
+
+@online{ampvis-intro,
+  author = {Kasper Skytte Andersen},
+  title = {Introduction to ampvis2},
+  url = {https://kasperskytte.github.io/ampvis2/articles/ampvis2.html#heatmap},
+  urldate = {2024-06-11}
+}
+
+@article{DeGooijer2006,
+  title = {25 years of time series forecasting},
+  volume = {22},
+  ISSN = {0169-2070},
+  url = {http://dx.doi.org/10.1016/j.ijforecast.2006.01.001},
+  DOI = {10.1016/j.ijforecast.2006.01.001},
+  number = {3},
+  journal = {International Journal of Forecasting},
+  publisher = {Elsevier BV},
+  author = {De Gooijer,  Jan G. and Hyndman,  Rob J.},
+  year = {2006},
+  month = jan,
+  pages = {443–473}
+}
+
+@article{Gotelli2001,
+  title = {Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness},
+  volume = {4},
+  ISSN = {1461-0248},
+  url = {http://dx.doi.org/10.1046/j.1461-0248.2001.00230.x},
+  DOI = {10.1046/j.1461-0248.2001.00230.x},
+  number = {4},
+  journal = {Ecology Letters},
+  publisher = {Wiley},
+  author = {Gotelli,  Nicholas J. and Colwell,  Robert K.},
+  year = {2001},
+  month = jul,
+  pages = {379–391}
+}