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Add Galaxy tutorial for breast cancer spatial transcriptomics analysis from Galaxy-EISTA #7025

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Add Galaxy tutorial for breast cancer spatial transcriptomics analysis from Galaxy-EISTA #7025

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3ed4429
Create spatial-brest-cancer-tme-EISTA tutorial
khaled196 Jun 25, 2026
ac2a16a
Merge branch 'galaxyproject:main' into eista
khaled196 Jul 6, 2026
43df93e
add the usecase to the tutirual needs quistions and testing
khaled196 Jul 6, 2026
2589008
Merge branch 'galaxyproject:main' into eista
khaled196 Jul 30, 2026
f2b3d79
add spatial tutorial
khaled196 Aug 4, 2026
7f73cf4
remove spatial from imaging
khaled196 Aug 4, 2026
0eadb15
Update topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/t…
khaled196 Aug 4, 2026
0e73d3f
Add spatial transcriptomics workflow test
khaled196 Aug 4, 2026
c5dc266
Update topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/t…
khaled196 Aug 4, 2026
9fc5547
Update topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/t…
khaled196 Aug 4, 2026
ac10818
remove test data and use zenodo and adress Amir comments
khaled196 Aug 4, 2026
8164ba1
add images
khaled196 Aug 4, 2026
8a1f13b
remove introduction header
khaled196 Aug 4, 2026
ab635af
change file names
khaled196 Aug 4, 2026
609ef97
Merge branch 'main' into eista
khaled196 Aug 4, 2026
d2dc863
update file name
khaled196 Aug 4, 2026
eb13d97
fix the name
khaled196 Aug 5, 2026
6668211
validate the tutorial manualy and update outptus
khaled196 Aug 6, 2026
8bda7dd
Remove image with newline in filename
khaled196 Aug 6, 2026
2f77497
update time 3h is enugh
khaled196 Aug 6, 2026
ab761d1
fix quistions hvg
khaled196 Aug 6, 2026
354000d
remove preserve the x as to counts
khaled196 Aug 6, 2026
37eb3db
cleaner table
khaled196 Aug 6, 2026
9b4589d
cleaner table
khaled196 Aug 6, 2026
ec81d7c
I will fix the rest later
khaled196 Aug 6, 2026
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42 changes: 42 additions & 0 deletions .../single-cell/images/spatial-breast-cancer-tme/eista_spatial_breast_workflow.svg
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43 changes: 43 additions & 0 deletions topics/single-cell/images/spatial-breast-cancer-tme/eista_tme_interpretation.svg
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@nilchia nilchia Aug 4, 2026

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Please change the "signals" from italic to normal.

The text in the box is outside of the box.

@nilchia nilchia Aug 5, 2026

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Thanks for changing. The genes should be italic. They are human genes, right?

@khaled196 khaled196 Aug 6, 2026

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Yes those are human genes. I removed them for now until find better annotating method.

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Binary file added topics/single-cell/images/spatial-breast-cancer-tme/executed_workflow_overview.png
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3 changes: 3 additions & 0 deletions topics/single-cell/metadata.yaml
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Expand Up @@ -95,6 +95,9 @@ subtopics:
- id: exploratory
title: "Exploratory Analyses"
description: "You have clusters and you have genes. What can you do now? Come here to explore your results more!"
- id: spatial
title: "Spatial transcriptomics"
description: "Tutorials for analysing spatially resolved gene expression data, integrating molecular measurements with tissue coordinates, morphology, spatial neighbourhoods, and cell-state annotations."


references:
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19 changes: 19 additions & 0 deletions topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/data-library.yaml
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@@ -0,0 +1,19 @@
---
destination:
type: library
name: GTN - Material
description: Galaxy Training Network Material
synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
items:
- name: Single Cell
description: Single-cell and spatial omics training material
items:
- name: Spatial transcriptomics of the breast cancer tumour microenvironment using EISTA Galaxy
items:
- name: 'DOI: 10.5281/zenodo.15129356'
description: BreastCancer1 Visium breast cancer training dataset
items:
- url: https://zenodo.org/api/records/15129356/files/BreastCancer1.zip/content
src: url
ext: zip
info: https://zenodo.org/records/15129356
3 changes: 3 additions & 0 deletions topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/faqs/index.md
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---
layout: faq-page
---
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