Merge pull request #4480 from hexhowells/NCBI-to-AnnData

New NCBI to AnnData tutorial
galaxyproject · Dec 13, 2023 · 9db8751 · 9db8751
2 parents 610e5d2 + 8622962
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diff --git a/_config.yml b/_config.yml
@@ -104,6 +104,7 @@ icon-tag:
   event: far fa-calendar
   feedback: far fa-comments
   galaxy-advanced-search: fas fa-angle-double-down
+  galaxy-show-active: fa fa-map-marker
   galaxy-barchart: fas fa-chart-bar
   galaxy-bug: fas fa-bug
   galaxy-chart-select-data: fas fa-database

diff --git a/topics/single-cell/images/scrna-ncbi-anndata/cell_metadata.png b/topics/single-cell/images/scrna-ncbi-anndata/cell_metadata.png
diff --git a/topics/single-cell/images/scrna-ncbi-anndata/clinical_info_spreadsheet.png b/topics/single-cell/images/scrna-ncbi-anndata/clinical_info_spreadsheet.png
diff --git a/topics/single-cell/images/scrna-ncbi-anndata/metadata.png b/topics/single-cell/images/scrna-ncbi-anndata/metadata.png
diff --git a/topics/single-cell/images/scrna-ncbi-anndata/patient_samples_paper.png b/topics/single-cell/images/scrna-ncbi-anndata/patient_samples_paper.png
diff --git a/topics/single-cell/images/scrna-ncbi-anndata/replicates_paper.png b/topics/single-cell/images/scrna-ncbi-anndata/replicates_paper.png
diff --git a/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.bib b/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.bib
@@ -0,0 +1,13 @@
+@article{Song2022,
+  title = {Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states},
+  volume = {13},
+  ISSN = {2041-1723},
+  url = {http://dx.doi.org/10.1038/s41467-021-27322-4},
+  DOI = {10.1038/s41467-021-27322-4},
+  number = {1},
+  journal = {Nature Communications},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Song,  Hanbing and Weinstein,  Hannah N. W. and Allegakoen,  Paul and Wadsworth,  Marc H. and Xie,  Jamie and Yang,  Heiko and Castro,  Ethan A. and Lu,  Kevin L. and Stohr,  Bradley A. and Feng,  Felix Y. and Carroll,  Peter R. and Wang,  Bruce and Cooperberg,  Matthew R. and Shalek,  Alex K. and Huang,  Franklin W.},
+  year = {2022},
+  month = jan
+}
diff --git a/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md b/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
diff --git a/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata-test.yml b/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata-test.yml
@@ -0,0 +1,49 @@
+- doc: Converting NCBI Data to the AnnData Format
+  job:
+    GSM5353214_PA_AUG_PB_1A_S1_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353214_PA_AUG_PB_1A_S1_dge.txt
+      filetype: tabular
+    GSM5353215_PA_AUG_PB_1B_S2_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353215_PA_AUG_PB_1B_S2_dge.txt
+      filetype: tabular
+    GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt
+      filetype: tabular
+    GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt
+      filetype: tabular
+    GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt
+      filetype: tabular
+    GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt
+      filetype: tabular
+    GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt
+      filetype: tabular
+    GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt
+      filetype: tabular
+    GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt
+      filetype: tabular
+    GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt:
+      class: File
+      location: https://zenodo.org/record/10101768/files/GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt
+      filetype: tabular
+  outputs:
+    obs:
+      asserts:
+        has_text:
+          text: "AAAGGGGAGTGT-0	0	nan	patient1	left-mid	AUG_PB1A	8165"
+        has_text:
+          text: "GGCAATTGGGAC-2	2	poolA	patient2	right-mid	MAY_PB1A	8848"