Workflow Type: Galaxy
Open
Frozen
Updated tool versions Aug 24 2022
Associated Tutorial
This workflows is part of the tutorial CS3_Filter, Plot and Explore Single-cell RNA-seq Data, available in the GTN
Thanks to...
Tutorial Author(s): Wendi Bacon
Tutorial Contributor(s): Helena Rasche, Julia Jakiela
Inputs
ID | Name | Description | Type |
---|---|---|---|
Mito-counted AnnData | #main/Mito-counted AnnData | n/a |
|
Steps
ID | Name | Description |
---|---|---|
1 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
2 | Scanpy FilterCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0 |
3 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
4 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
5 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
6 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
7 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
8 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
9 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
10 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
11 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
12 | Scanpy FilterCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0 |
13 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
14 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
15 | Scanpy FilterCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0 |
16 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
17 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
18 | Scanpy FilterGenes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0 |
19 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
20 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
21 | Scanpy NormaliseData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0 |
22 | Scanpy FindVariableGenes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0 |
23 | Scanpy ScaleData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0 |
24 | Scanpy RunPCA | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0 |
25 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
26 | Scanpy ComputeGraph | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1 |
27 | Scanpy RunTSNE | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1 |
28 | Scanpy RunUMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0 |
29 | Scanpy FindCluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0 |
30 | Scanpy FindMarkers | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0 |
31 | Scanpy FindMarkers | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0 |
32 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 |
33 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 |
34 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
35 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 |
36 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
37 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0 |
38 | Join two Datasets | join1 |
39 | Join two Datasets | join1 |
40 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0 |
41 | Cut | Cut1 |
42 | Cut | Cut1 |
43 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Counts-filtered Object | #main/Counts-filtered Object | n/a |
|
Filtered Object | #main/Filtered Object | n/a |
|
Final cell annotated object | #main/Final cell annotated object | n/a |
|
Final object | #main/Final object | n/a |
|
General - Filterbycounts | #main/General - Filterbycounts | n/a |
|
General - Filterbygenes | #main/General - Filterbygenes | n/a |
|
General - Filterbymito | #main/General - Filterbymito | n/a |
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General - Filtered object | #main/General - Filtered object | n/a |
|
Genes-filtered Object | #main/Genes-filtered Object | n/a |
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Markers - cluster | #main/Markers - cluster | n/a |
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Markers - cluster - named | #main/Markers - cluster - named | n/a |
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Markers - genotype | #main/Markers - genotype | n/a |
|
Markers - genotype - named | #main/Markers - genotype - named | n/a |
|
Mito-filtered Object | #main/Mito-filtered Object | n/a |
|
PCA Variance | #main/PCA Variance | n/a |
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Scatter - genes x UMIs | #main/Scatter - genes x UMIs | n/a |
|
Scatter - mito x UMIs | #main/Scatter - mito x UMIs | n/a |
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Scatter - mito x genes | #main/Scatter - mito x genes | n/a |
|
Violin - Filterbycounts | #main/Violin - Filterbycounts | n/a |
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Violin - Filterbygenes | #main/Violin - Filterbygenes | n/a |
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Violin - Filterbymito | #main/Violin - Filterbymito | n/a |
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Violin - batch - log | #main/Violin - batch - log | n/a |
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Violin - genotype - log | #main/Violin - genotype - log | n/a |
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Violin - sex - log | #main/Violin - sex - log | n/a |
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_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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_anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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_anonymous_output_13 | #main/_anonymous_output_13 | n/a |
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_anonymous_output_14 | #main/_anonymous_output_14 | n/a |
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_anonymous_output_15 | #main/_anonymous_output_15 | n/a |
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_anonymous_output_16 | #main/_anonymous_output_16 | n/a |
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_anonymous_output_17 | #main/_anonymous_output_17 | n/a |
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_anonymous_output_18 | #main/_anonymous_output_18 | n/a |
|
_anonymous_output_19 | #main/_anonymous_output_19 | n/a |
|
_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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_anonymous_output_20 | #main/_anonymous_output_20 | n/a |
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_anonymous_output_21 | #main/_anonymous_output_21 | n/a |
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_anonymous_output_22 | #main/_anonymous_output_22 | n/a |
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_anonymous_output_23 | #main/_anonymous_output_23 | n/a |
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_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master
783e51f
3.0 (earliest) Created 25th Jun 2024 at 11:12 by Helena Rasche
Added/updated 4 files
Frozen
3.0
2ccda89
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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Discussion Channel
Tool
Activity
Views: 193 Downloads: 86
Created: 25th Jun 2024 at 11:12
Last updated: 25th Jun 2024 at 11:12
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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