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lines changed Original file line number Diff line number Diff line change @@ -30,7 +30,7 @@ During this workshop, you will use conda environments to run the exercises. This
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| <img border =" 0 " src =" https://cdn0.iconfinder.com/data/icons/network-analysis-7/64/cluster-positive-negative-group-collection-512.png " width =" 30 " height =" 30 " > Clustering | [ Seurat_clust] ( labs/compiled/seurat/seurat_04_clustering.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/seurat/seurat_04_clustering.Rmd ) ) | [ Scater_clust] ( labs/compiled/scater/scater_04_clustering.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scater/scater_04_clustering.Rmd ) ) | [ Scanpy_clust] ( labs/compiled/scanpy/scanpy_04_clustering.html ) ([ .ipynb] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scanpy/scanpy_04_clustering.ipynb ) ) |
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| <img border =" 0 " src =" https://static.thenounproject.com/png/1517975-200.png " width =" 30 " height =" 30 " > Differential expression | [ Seurat_dge] ( labs/compiled/seurat/seurat_05_dge.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/seurat/seurat_05_dge.Rmd ) ) | [ Scater_dge] ( labs/compiled/scater/scater_05_dge.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scater/scater_05_dge.Rmd ) ) | [ Scanpy_dge] ( labs/compiled/scanpy/scanpy_05_dge.html ) ([ .ipynb] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scanpy/scanpy_05_dge.ipynb ) ) |
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| <img border =" 0 " src =" files/icon_celltype.png " width =" 30 " height =" 30 " > Celltype prediction | [ Seurat_ct] ( labs/compiled/seurat/seurat_06_celltype.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/seurat/seurat_06_celltype.Rmd ) ) | [ Scater_ct] ( labs/compiled/scater/scater_06_celltype.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scater/scater_06_celltype.Rmd ) ) | [ Scanpy_ct] ( labs/compiled/scanpy/scanpy_06_celltype.html ) ([ .ipynb] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scanpy/scanpy_06_celltype.ipynb ) ) |
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- | <img border =" 0 " src =" files/ST_icon.png " width =" 30 " height =" 30 " > Spatial transcriptomics | [ Seurat_ST] ( labs/compiled/seurat/seurat_07_spatial.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/seurat/seurat_07_spatial.Rmd ) ) | [ Scater_ct ] ( labs/compiled/scater/scater_07_spatial.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scater/scater_07_spatial.Rmd ) ) | [ Scanpy_ST] ( labs/compiled/scanpy/scanpy_07_spatial.html ) ([ .ipynb] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scanpy/scanpy_07_spatail.ipynb ) ) |
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+ | <img border =" 0 " src =" files/ST_icon.png " width =" 30 " height =" 30 " > Spatial transcriptomics | [ Seurat_ST] ( labs/compiled/seurat/seurat_07_spatial.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/seurat/seurat_07_spatial.Rmd ) ) | [ Scater_ST ] ( labs/compiled/scater/scater_07_spatial.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scater/scater_07_spatial.Rmd ) ) | [ Scanpy_ST] ( labs/compiled/scanpy/scanpy_07_spatial.html ) ([ .ipynb] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/scanpy/scanpy_07_spatail.ipynb ) ) |
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| <img border =" 0 " src =" https://cdn2.vectorstock.com/i/1000x1000/49/51/route-location-icon-vector-16394951.jpg " width =" 30 " height =" 30 " > Trajectory inference | [ Slingshot_ti] ( labs/compiled/slingshot/slingshot.html ) ([ .Rmd] ( https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/compiled/slingshot/slingshot.Rmd ) ) | [ Slingshot_ti] ( labs/compiled/slingshot/slingshot.html ) | [ PAGA_ti] ( https://scanpy-tutorials.readthedocs.io/en/latest/paga-paul15.html ) |
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