Merge pull request #4393 from nomadscientist/branch_sc_v3_squashed

remove spanish slide deck
add single cell tags and reorder
update tags and standardize titles
fix case study reloaded tags
fix deconvolution tags
add epigenetics tag
fix tips tags
add CoP page to 'contribute' section
create Galaxy Single Cell community FAQ
add single cell omics instance FAQ
categorize FAQ
fix image reference
fix matrix badge
test single cell specific faq in a tutorial
faq path fixv1
fix symbols
get badge inline
add user community channel faq everywhere
add single_cell_omics ref
fix linting errors
standardise symbols
add data management tags

topics/single-cell/faqs/single_cell_omics.md

@@ -0,0 +1,15 @@
+---
+title: Use our single cell Galaxy instance
+area: Resources
+box_type: tip
+layout: faq
+contributors: [nomadscientist]
+---
+
+Did you know we have a unique Galaxy instance with all our single cell tools highlighted to make it easier to use? We recommend this instance for all your single cell analysis needs, particularly for newer users.
+
+This **subdomain** is uses the main European Galaxy infrastructure and power, it's just organised better for users of particular analyses...like single cell!
+
+Try it out! All your histories/workflows/logins from the general [European Galaxy instance](https://usegalaxy.eu) will be there!
+
+ - <i class="fa fa-tv" aria-hidden="true"></i> [Single cell omics Galaxy instance](https://singlecell.usegalaxy.eu)

topics/single-cell/faqs/user_community_join.md

@@ -0,0 +1,13 @@
+---
+title: How can I talk with other users?
+area: Community
+box_type: tip
+layout: faq
+contributors: [nomadscientist]
+---
+
+To discuss with like-minded scientists, join our Matrix/Element chatroom to discuss with fellow users of Galaxy single cell analysis tools!
+
+[![Matrix](/training-material/topics/single-cell/images/matrix-badge.svg)](https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im)
+
+We also post new tutorials / workflows there from time to time, as well as any other news.

topics/single-cell/index.md

@@ -7,5 +7,6 @@ topic_name: single-cell
 
 If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single Cell Community of Practice!
 
- - <i class="fa fa-external-link-alt" aria-hidden="true"></i> [Matrix Chat Forum](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows:gitter.im)
+ - <i class="fa fa-hand-o-right" aria-hidden="true"></i> [Community of Practice](https://galaxyproject.org/projects/singlecell/)
+ - <i class="fa fa-comments-o" aria-hidden="true"></i> [Matrix Chat Forum](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows:gitter.im)
  - <i class="fa fa-envelope" aria-hidden="true"> </i> [Mailing List](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/)

topics/single-cell/metadata.yaml

@@ -4,8 +4,8 @@ type: use
 title: Single Cell
 summary: |
   Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!). When you generate your lovely gene lists for your cells, consider checking out our Transcriptomics tutorials for further network analysis!
-  
-  What else do you want to see? You can submit tool and/or tutorial request on our [Single Cell Community Tool Request Spreadsheet](https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing).
+
+  What else do you want to see? You can submit tool and/or tutorial request on our <i class="fa fa-wrench" aria-hidden="true"></i> [Single Cell Community Tool Request Spreadsheet](https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing).
    {: .alert.alert-success}
 #docker_image: "quay.io/galaxy/transcriptomics-training"
 

topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.md

@@ -38,10 +38,8 @@ follow_up_training:
 
 tags:
   - single-cell
-  - human
-  - deconvolution
-  - bulk
   - transcriptomics
+  - data management
 ---
 
 
@@ -424,3 +422,5 @@ You have successfully performed, essentially, three workflows. You can find the
 With these workflows, you've created three Expression Set objects, capable of running in the MuSiC Compare tutorial. Now you just need the bulk RNA-seq Expression Set objects!
 
 This tutorial is part of the [https://singlecell.usegalaxy.eu](https://singlecell.usegalaxy.eu) portal ({% cite tekman2020single %}).
+
+{% snippet topics/single-cell/faqs/user_community_join.md %}

topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.md

@@ -3,7 +3,7 @@ layout: tutorial_hands_on
 subtopic: datamanipulation
 priority: 2
 
-title: Bulk matrix to ESet object | Creating the bulk RNA-seq dataset for deconvolution
+title: Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
 zenodo_link: 'https://zenodo.org/record/7319173'
 questions:
 - Where can I find good quality RNA-seq datasets?
@@ -26,10 +26,8 @@ contributions:
 
 tags:
   - single-cell
-  - human
-  - deconvolution
-  - bulk
   - transcriptomics
+  - data management
 
 requirements:
   -
@@ -304,3 +302,5 @@ You can find the [workflow for generating the ESet object](https://usegalaxy.eu/
 ![7 boxes in the workflow editor and a subworkflow box for converting Ensembl to GeneSymbol](../../images/bulk-music/workflow-bulk.png "Workflow: Generating the bulk ESet Objects")
 
 This tutorial is part of the [https://singlecell.usegalaxy.eu](https://singlecell.usegalaxy.eu) portal ({% cite tekman2020single %}).
+
+{% snippet topics/single-cell/faqs/user_community_join.md %}

topics/single-cell/tutorials/bulk-music-4-compare/tutorial.md

@@ -6,10 +6,6 @@ title: Comparing inferred cell compositions using MuSiC deconvolution
 zenodo_link: https://zenodo.org/record/7319925
 tags:
   - single-cell
-  - mouse
-  - human
-  - deconvolution
-  - bulk
   - transcriptomics
 questions:
 - How do the cell type distributions vary in bulk RNA samples across my variable of interest?
@@ -63,7 +59,7 @@ In the standard MuSiC tutorial, we used human pancreas data. We will now use the
 
 ![Three colours of arrows connect bulk healthy & diseased data sets to a combined single cell (altogether); bulk healthy and single cell healthy & bulk diseased with single cell diseased (like4like); and bulk diseased and healthy with the single cell healthy reference (healthyscref).](../../images/bulk-music/comparison.png "Plan of analysis")
 
-If you have followed the previous tutorials, you will have built your [single cell ESet object]({% link topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.md %}) and your [bulk ESet object]({% link topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.md %}), then you can copy these into a new history now. Otherwise, follow the steps below to import the datasets you'll need. 
+If you have followed the previous tutorials, you will have built your [single cell ESet object]({% link topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.md %}) and your [bulk ESet object]({% link topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.md %}), then you can copy these into a new history now. Otherwise, follow the steps below to import the datasets you'll need.
 
 {% snippet  faqs/galaxy/histories_copy_dataset.md %}
 
@@ -281,3 +277,5 @@ Congrats! You've made it to the end of this suite of deconvolution tutorials! Yo
 ![Workflow editor showing 5 inputs and 3 runs of the MuSiC Compare tool](../../images/bulk-music/compare_workflow.png "MuSiC Compare Tutorial Workflow")
 
 This tutorial is part of the [https://singlecell.usegalaxy.eu](https://singlecell.usegalaxy.eu) portal ({% cite tekman2020single %}).
+
+{% snippet topics/single-cell/faqs/user_community_join.md %}

topics/single-cell/tutorials/bulk-music/tutorial.md

@@ -8,10 +8,6 @@ priority: 1
 zenodo_link: https://zenodo.org/record/5719228
 tags:
   - single-cell
-  - mouse
-  - human
-  - deconvolution
-  - bulk
   - transcriptomics
 questions:
 - How do we infer cell type proportions from bulk RNA-seq data?
@@ -285,7 +281,7 @@ For now we need to construct our Expression set objects that will be consumed by
 
 Here we shall build two ExpressionSet objects corresponding to the bulk and single-cell datatypes.
 
-### **Construct Expression Set Object**
+### Construct Expression Set Object
 
 > <hands-on-title>Build the Expression Set inputs</hands-on-title>
 >
@@ -304,7 +300,7 @@ Here we shall build two ExpressionSet objects corresponding to the bulk and sing
 >
 {: .hands_on}
 
-#### **Inspect Expression Set Object**
+#### Inspect Expression Set Object
 
 We will now inspect these objects we just created to see what information we can extract out of them, and how these multiple datasets are summarized within the object.
 
@@ -511,7 +507,7 @@ Both the MuSiC and the NNLS calculations of this data is best represented in the
 
 You will need to again create ExpressionSet objects, as before.
 
-### **Construct Expression Set Object**
+### Construct Expression Set Object
 
 > <hands-on-title>Build the Expression Set inputs</hands-on-title>
 >
@@ -666,3 +662,5 @@ Note how two ExpressionSet objects are constructed: one from bulk RNA-seq tabula
 ![workflow_dendro.png](../../images/bulk-music/workflow_dendro.png "Workflow for generating a dendrogram and clustering cells upon it")
 
 This tutorial is part of the [https://singlecell.usegalaxy.eu](https://singlecell.usegalaxy.eu) portal ({% cite tekman2020single %}).
+
+{% snippet topics/single-cell/faqs/user_community_join.md %}