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

topics/single-cell/metadata.yaml

@@ -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:

topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/data-library.yaml

@@ -0,0 +1,14 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material
+items:
+- name: Spatial transcriptomics analysis of a breast cancer section in Galaxy
+  description: Prepared SpatialData input derived from the 10x Genomics Human Breast Cancer, Block A Section 1 dataset
+  items:
+  - url: https://zenodo.org/api/records/21792657/files/V1_Breast_Cancer_Block_A_Section_1.spatialdata.zip/content
+    src: url
+    ext: spatialdata.zip
+    info: https://zenodo.org/records/21792657

topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/single-cell/tutorials/spatial-breast-cancer-tme-EISTA/tutorial.bib

@@ -0,0 +1,212 @@
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {Batut, B{\'{e}}r{\'{e}}nice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Gu{\'{e}}guen, Loraine and \v{C}ech, Martin and Chilton, John and Clements, Dave and Doppelt-Azeroual, Olivia and Erxleben, Anika and Freeberg, Mallory Ann and Gladman, Simon and Hoogstrate, Youri and Hotz, Hans-Rudolf and Houwaart, Torsten and Jagtap, Pratik and Larivi{\`{e}}re, Delphine and Le Corguill{\'{e}}, Gildas and Manke, Thomas and Mareuil, Fabien and Ram{\'{i}}rez, Fidel and Ryan, Devon and Sigloch, Florian Christoph and Soranzo, Nicola and Wolff, Joachim and Videm, Pavankumar and Wolfien, Markus and Wubuli, Aisanjiang and Yusuf, Dilmurat and Taylor, James and Backofen, Rolf and Nekrutenko, Anton and Gr{\"{u}}ning, Bj{\"{o}}rn},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author = {{GTN community}},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2026-07-06}
+}
+
+@online{TenXBreastCancerBlockA,
+  author = {{10x Genomics}},
+  title = {Human Breast Cancer (Block A Section 1) Spatial Gene Expression dataset},
+  year = {2020},
+  url = {https://www.10xgenomics.com/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0},
+  urldate = {2026-08-05}
+}
+
+@article{Wolf2018Scanpy,
+  doi = {10.1186/s13059-017-1382-0},
+  url = {https://doi.org/10.1186/s13059-017-1382-0},
+  year = {2018},
+  month = feb,
+  publisher = {Springer Science and Business Media LLC},
+  volume = {19},
+  number = {1},
+  author = {Wolf, F. Alexander and Angerer, Philipp and Theis, Fabian J.},
+  title = {{SCANPY}: large-scale single-cell gene expression data analysis},
+  journal = {Genome Biology}
+}
+
+@article{Virshup2024AnnData,
+  doi = {10.21105/joss.04371},
+  url = {https://doi.org/10.21105/joss.04371},
+  year = {2024},
+  publisher = {The Open Journal},
+  volume = {9},
+  number = {101},
+  pages = {4371},
+  author = {Virshup, Isaac and Rybakov, Sergei and Theis, Fabian J. and Angerer, Philipp and Wolf, F. Alexander},
+  title = {anndata: Access and store annotated data matrices},
+  journal = {Journal of Open Source Software}
+}
+
+@article{Marconato2024SpatialData,
+  doi = {10.1038/s41592-024-02212-x},
+  url = {https://doi.org/10.1038/s41592-024-02212-x},
+  year = {2024},
+  publisher = {Springer Science and Business Media LLC},
+  volume = {21},
+  pages = {2196--2209},
+  author = {Marconato, Luca and Palla, Giovanni and Yamauchi, Kevin A. and Virshup, Isaac and Heumos, Lukas and Treis, Tim and Vierdag, Wouter-Michiel and Huang, Xiaojie and Eze, Valentine C. and Papatheodorou, Irene and Rozenblatt-Rosen, Orit and Regev, Aviv and Theis, Fabian J. and Stegle, Oliver},
+  title = {{SpatialData}: an open and universal data framework for spatial omics},
+  journal = {Nature Methods}
+}
+
+@article{Palla2022Squidpy,
+  doi = {10.1038/s41592-021-01358-2},
+  url = {https://doi.org/10.1038/s41592-021-01358-2},
+  year = {2022},
+  publisher = {Springer Science and Business Media LLC},
+  volume = {19},
+  pages = {171--178},
+  author = {Palla, Giovanni and Spitzer, Hannah and Klein, Michal and others},
+  title = {Squidpy: a scalable framework for spatial omics analysis},
+  journal = {Nature Methods}
+}
+
+@article{Xu2023CellTypist,
+  doi = {10.1016/j.cell.2023.11.026},
+  url = {https://doi.org/10.1016/j.cell.2023.11.026},
+  year = {2023},
+  publisher = {Elsevier BV},
+  volume = {186},
+  number = {26},
+  pages = {5876--5891.e20},
+  author = {Xu, Chuan and Prete, Martin and Webb, Simone and Jardine, Laura and Stewart, Benjamin J. and Hoo, Regina and He, Peng and Meyer, Kerstin B. and Teichmann, Sarah A.},
+  title = {Automatic cell-type harmonization and integration across Human Cell Atlas datasets},
+  journal = {Cell}
+}
+
+@online{CellTypistDocs,
+  author = {{CellTypist developers}},
+  title = {CellTypist: automated cell type annotation for scRNA-seq datasets},
+  url = {https://www.celltypist.org/},
+  urldate = {2026-07-06}
+}
+
+@article{Dimitrov2022Liana,
+  doi = {10.1038/s41467-022-30755-0},
+  url = {https://doi.org/10.1038/s41467-022-30755-0},
+  year = {2022},
+  publisher = {Springer Science and Business Media LLC},
+  volume = {13},
+  number = {1},
+  pages = {3224},
+  author = {Dimitrov, Daniel and T{\"u}rei, D{\'{e}}nes and Garrido-Rodriguez, Mart{\'{i}}n and others},
+  title = {Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data},
+  journal = {Nature Communications}
+}
+
+@article{Dimitrov2024LianaPlus,
+  doi = {10.1038/s41556-024-01469-w},
+  url = {https://doi.org/10.1038/s41556-024-01469-w},
+  year = {2024},
+  publisher = {Springer Science and Business Media LLC},
+  volume = {26},
+  pages = {1613--1622},
+  author = {Dimitrov, Daniel and Schaefer, Martin H. and others},
+  title = {{LIANA+} provides an all-in-one framework for cell-cell communication inference},
+  journal = {Nature Cell Biology}
+}
+
+@article{Janesick2023BreastTME,
+  doi = {10.1038/s41467-023-43458-x},
+  url = {https://doi.org/10.1038/s41467-023-43458-x},
+  year = {2023},
+  publisher = {Springer Science and Business Media LLC},
+  volume = {14},
+  pages = {8353},
+  author = {Janesick, Amanda and Shelansky, Robert and Gottscho, Andrew D. and others},
+  title = {High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis},
+  journal = {Nature Communications}
+}
+
+@article{Wang2024TNBCSpatial,
+  doi = {10.1038/s41467-024-54145-w},
+  url = {https://doi.org/10.1038/s41467-024-54145-w},
+  year = {2024},
+  publisher = {Springer Science and Business Media LLC},
+  volume = {15},
+  pages = {10232},
+  author = {Wang, Xiaoyan and Venet, David and Lifrange, Fanny and others},
+  title = {Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications},
+  journal = {Nature Communications}
+}
+
+@article{Mehraj2021BreastTME,
+  author = {Mehraj, Umar and Ganai, Rais A. and Macha, Muzafar A. and Hamid, Abid and Zargar, Mohammed A. and Bhat, Ajaz A. and Nasser, Mohd Wasim and Haris, Mohammad and Batra, Surinder K. and Alshehri, Badr and Al-Baradie, Raed S. and Mir, Mohammad A. and Wani, Nisar A.},
+  title = {The tumor microenvironment as driver of stemness and therapeutic resistance in breast cancer: New challenges and therapeutic opportunities},
+  journal = {Cellular Oncology},
+  year = {2021},
+  volume = {44},
+  number = {6},
+  pages = {1209--1229},
+  doi = {10.1007/s13402-021-00634-9},
+  url = {https://doi.org/10.1007/s13402-021-00634-9}
+}
+
+@article{Croizer2024SpatialCAF,
+  author = {Croizer, Hugo and Mhaidly, Rana and Kieffer, Yann and Gentric, Geraldine and Djerroudi, Lounes and Leclere, Renaud and Pelon, Floriane and Robley, Catherine and Bohec, Mylene and Meng, Arnaud and Meseure, Didier and Romano, Emanuela and Baulande, Sylvain and Peltier, Agathe and Vincent-Salomon, Anne and Mechta-Grigoriou, Fatima},
+  title = {Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancer},
+  journal = {Nature Communications},
+  year = {2024},
+  volume = {15},
+  pages = {2806},
+  doi = {10.1038/s41467-024-47068-z},
+  url = {https://doi.org/10.1038/s41467-024-47068-z}
+}
+
+@article{Stahl2016SpatialTranscriptomics,
+  author = {St{\aa}hl, Patrik L. and Salm{\'e}n, Fredrik and Vickovic, Sanja and Lundmark, Anna and Fern{\'a}ndez Navarro, Jos{\'e} and Magnusson, Jens and Giacomello, Stefania and Asp, Michaela and Westholm, Jakub O. and Huss, Mikael and Mollbrink, Annelie and Linnarsson, Sten and Codeluppi, Simone and Borg, {\AA}ke and Pont{\'e}n, Fredrik and Costea, Paul Igor and Sahl{\'e}n, Pelin and Mulder, Jan and Bergmann, Olaf and Lundeberg, Joakim and Fris{\'e}n, Jonas},
+  title = {Visualization and analysis of gene expression in tissue sections by spatial transcriptomics},
+  journal = {Science},
+  year = {2016},
+  volume = {353},
+  number = {6294},
+  pages = {78--82},
+  doi = {10.1126/science.aaf2403},
+  url = {https://doi.org/10.1126/science.aaf2403}
+}
+
+@article{Rao2021TissueArchitecture,
+  author = {Rao, Anjali and Barkley, Dalia and Fran{\c{c}}a, Gustavo S. and Yanai, Itai},
+  title = {Exploring tissue architecture using spatial transcriptomics},
+  journal = {Nature},
+  year = {2021},
+  volume = {596},
+  pages = {211--220},
+  doi = {10.1038/s41586-021-03634-9},
+  url = {https://doi.org/10.1038/s41586-021-03634-9}
+}
+
+
+@article{Kumar2023HumanBreastAtlas,
+  author = {Kumar, Tapsi and Nee, Kevin and Wei, Runmin and He, Siyuan and Nguyen, Quy H. and others},
+  title = {A spatially resolved single-cell genomic atlas of the adult human breast},
+  journal = {Nature},
+  year = {2023},
+  volume = {620},
+  pages = {181--191},
+  doi = {10.1038/s41586-023-06252-9},
+  url = {https://doi.org/10.1038/s41586-023-06252-9}
+}
+
+@online{CellTypistModels,
+  author = {{CellTypist developers}},
+  title = {CellTypist model list},
+  url = {https://www.celltypist.org/models},
+  urldate = {2026-08-05}
+}