Filter plot and explore single-cell RNA-seq data with Scanpy (imported from uploaded file)
1.0

Workflow Type: Galaxy

Inputs

ID Name Description Type
Batched_AnnData #main/Batched_AnnData The output from this tutorial: https://training.galaxyproject.org/training-material//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html This is an AnnData object that has a column declaring which genes are mitochondrial or not.
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Steps

ID Name Description
1 QC_AnnData toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy2
2 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
3 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
4 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
5 Scanpy filter toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
6 Violin_log_genotype toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
7 Violin_log_sex toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
8 Scatter_GenesxUMI toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
9 Violin_log_batch toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
10 Scatter_GenesxMito toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
11 Scatter_UMIxMito toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
12 Genes_Filtered_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
13 Violin_log_genotype-Genes toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
14 Scanpy filter toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
15 UMI_Filtered_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
16 Violin_log_genotype-UMIs toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
17 Mito_Filtered_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
18 Violin_log_genotype-Mito toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
19 Cells_Filtered_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
20 Normalised_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0
21 Logarithmised_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
22 Frozen_Object toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1
23 FVG_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
24 Scaled_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
25 PCA_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2
26 PCA_Variance_Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
27 Neighbours_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
28 tSNE_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2
29 UMAP_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2
30 Clustered_Object toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2
31 DEGs-Genotype toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
32 DEGs-Louvain toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
33 tSNE_Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
34 PCA_Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
35 UMAP_Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
36 Annotated_Object toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1
37 Annotated_Plots toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2

Outputs

ID Name Description Type
Annotated_Object #main/Annotated_Object n/a
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Annotated_Plots #main/Annotated_Plots n/a
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Cells_Filtered_Object #main/Cells_Filtered_Object n/a
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Clustered_Object #main/Clustered_Object n/a
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FVG_Object #main/FVG_Object n/a
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Frozen_Object #main/Frozen_Object n/a
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Genes_Filtered_Object #main/Genes_Filtered_Object n/a
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Genes_Part_Object #main/Genes_Part_Object n/a
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Logarithmised_Object #main/Logarithmised_Object n/a
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Mito_Filtered_Object #main/Mito_Filtered_Object n/a
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Neighbours_Object #main/Neighbours_Object n/a
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Normalised_Object #main/Normalised_Object n/a
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PCA_Object #main/PCA_Object n/a
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PCA_Plot #main/PCA_Plot n/a
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PCA_Variance_Plot #main/PCA_Variance_Plot n/a
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QC_Object #main/QC_Object n/a
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Ranked_Genes-Cluster #main/Ranked_Genes-Cluster n/a
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Ranked_Genes-by_Genotype #main/Ranked_Genes-by_Genotype n/a
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Scaled_Object #main/Scaled_Object n/a
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Scatter_GenesxMito #main/Scatter_GenesxMito n/a
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Scatter_GenesxUMI #main/Scatter_GenesxUMI n/a
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Scatter_UMIxMito #main/Scatter_UMIxMito n/a
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UMAP_Object #main/UMAP_Object n/a
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UMAP_Plot #main/UMAP_Plot n/a
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UMI_Filtered_Object #main/UMI_Filtered_Object n/a
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UMI_Part_Object #main/UMI_Part_Object n/a
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Violin_log_batch #main/Violin_log_batch n/a
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Violin_log_genotype #main/Violin_log_genotype n/a
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Violin_log_genotype-Genes #main/Violin_log_genotype-Genes n/a
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Violin_log_genotype-Mito #main/Violin_log_genotype-Mito n/a
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Violin_log_genotype-UMIs #main/Violin_log_genotype-UMIs n/a
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Violin_log_sex #main/Violin_log_sex n/a
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anndata_out #main/anndata_out n/a
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general #main/general n/a
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obs #main/obs n/a
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tSNE_Object #main/tSNE_Object n/a
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tSNE_Plot #main/tSNE_Plot n/a
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var #main/var n/a
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Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:56 by GTN Bot

Added/updated 4 files


Open master c855110
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Created: 2nd Jun 2025 at 10:56

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