Merge pull request #5491 from MarisaJL/seurat_pbmc

Adding Seurat version of the PBMC clustering tutorial

Author: pavanvidem

topics/single-cell/images/scrna-seurat-pbmc3k/seurat_DoHeatmap_CellType_markers.png

@@ -0,0 +1,27 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Transcriptomics
+  description: Training material for all kinds of transcriptomics analysis.
+  items:
+  - name: Clustering 3K PBMCs with Scanpy
+    items:
+    - name: 'DOI: 10.5281/zenodo.3581213'
+      description: latest
+      items:
+      - url: https://zenodo.org/api/files/78a8ec7e-3357-44b8-854d-4a9d772b4589/barcodes.tsv
+        src: url
+        ext: tsv
+        info: https://zenodo.org/record/3581213
+      - url: https://zenodo.org/api/files/78a8ec7e-3357-44b8-854d-4a9d772b4589/genes.tsv
+        src: url
+        ext: tsv
+        info: https://zenodo.org/record/3581213
+      - url: https://zenodo.org/api/files/78a8ec7e-3357-44b8-854d-4a9d772b4589/matrix.mtx
+        src: url
+        ext: mtx
+        info: https://zenodo.org/record/3581213

topics/single-cell/images/scrna-seurat-pbmc3k/seurat_DoHeatmap_CellType_markers_SCT.png

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+@Article{seurat2023v5,
+  author = {Yuhan Hao and Tim Stuart and Madeline H Kowalski and Saket Choudhary and Paul Hoffman and Austin Hartman and Avi Srivastava and Gesmira Molla and Shaista Madad and Carlos Fernandez-Granda and Rahul Satija},
+  title = {Dictionary learning for integrative, multimodal and scalable single-cell analysis},
+  journal = {Nature Biotechnology},
+  year = {2023},
+  doi = {10.1038/s41587-023-01767-y},
+  url = {https://doi.org/10.1038/s41587-023-01767-y},
+}
+
+@article{SCTransform2022, 
+title={Comparison and evaluation of statistical error models for scrna-seq}, 
+DOI={10.1186/s13059-021-02584-9},
+volume={23}, 
+number={1}, 
+journal={Genome Biology}, 
+author={Choudhary, Saket and Satija, Rahul}, 
+year={2022}, 
+month={Jan}} 
+
+@article{tekman2020single,
+  title={A single-cell RNA-sequencing training and analysis suite using the Galaxy framework},
+  author={Tekman, Mehmet and Batut, B{\'e}r{\'e}nice and Ostrovsky, Alexander and Antoniewski, Christophe and Clements, Dave and Ramirez, Fidel and Etherington, Graham J and Hotz, Hans-Rudolf and Scholtalbers, Jelle and Manning, Jonathan R and others},
+  journal={GigaScience},
+  DOI={10.1093/gigascience/giaa102},
+  volume={9},
+  number={10},
+  pages={giaa102},
+  year={2020},
+  publisher={Oxford University Press}
+}

topics/single-cell/images/scrna-seurat-pbmc3k/seurat_DoHeatmap_TopPositiveMarkers.png

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+- doc: Test the Clustering 3k PBMCs with Seurat tutorial with separate preprocessing steps
+  job:
+    matrix.mtx:
+      class: File
+      location: https://zenodo.org/records/3581213/files/matrix.mtx
+      filetype: mtx
+    genes.tsv:
+      class: File
+      location: https://zenodo.org/records/3581213/files/genes.tsv
+      filetype: tsv
+    barcodes.tsv:
+      class: File
+      location: https://zenodo.org/records/3581213/files/barcodes.tsv
+      filetype: tsv
+    Canonical Markers:
+      class: File
+      location: https://zenodo.org/records/14013475/files/Canonical_Markers.tabular
+      filetype: tabular
+  outputs:
+    Input 3k PBMC:
+      location: https://zenodo.org/records/14013475/files/Input_3k_PBMC.rds
+      compare: diff
+    Preprocessed Data:
+      location: https://zenodo.org/records/14013475/files/Preprocessed_Data.rds
+      compare: diff
+    Annotated Clusters:
+      location: https://zenodo.org/records/14013475/files/Annotated_Clusters.rds
+      compare: diff
+    Input DE Markers:
+      location: https://zenodo.org/records/14013475/files/Input_DE_Markers.tabular
+      compare: diff