Filter, Plot and Explore Single-cell RNA-seq Data updated
Version 1

Visit source Download RO Crate
Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/1017?version=1

Inputs

ID Name Description Type
Mito-counted AnnData #main/Mito-counted AnnData n/a
  • File

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+galaxy9
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+galaxy9
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+galaxy9
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+galaxy9
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+galaxy9
22 Scanpy FindVariableGenes toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9
23 Scanpy ScaleData toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9
24 Scanpy RunPCA toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9
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+galaxy9
27 Scanpy RunTSNE toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9
28 Scanpy RunUMAP toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9
29 Scanpy FindCluster toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9
30 Scanpy FindMarkers toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9
31 Scanpy FindMarkers toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9
32 Scanpy PlotEmbed toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
33 Scanpy PlotEmbed toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
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+galaxy9
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+galaxy91
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+galaxy91
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+galaxy9

Outputs

ID Name Description Type
Counts-filtered Object #main/Counts-filtered Object n/a
  • File
Filtered Object #main/Filtered Object n/a
  • File
Final cell annotated object #main/Final cell annotated object n/a
  • File
Final object #main/Final object n/a
  • File
General - Filterbycounts #main/General - Filterbycounts n/a
  • File
General - Filterbygenes #main/General - Filterbygenes n/a
  • File
General - Filterbymito #main/General - Filterbymito n/a
  • File
General - Filtered object #main/General - Filtered object n/a
  • File
Genes-filtered Object #main/Genes-filtered Object n/a
  • File
Markers - cluster #main/Markers - cluster n/a
  • File
Markers - cluster - named #main/Markers - cluster - named n/a
  • File
Markers - genotype #main/Markers - genotype n/a
  • File
Markers - genotype - named #main/Markers - genotype - named n/a
  • File
Mito-filtered Object #main/Mito-filtered Object n/a
  • File
PCA Variance #main/PCA Variance n/a
  • File
Scatter - genes x UMIs #main/Scatter - genes x UMIs n/a
  • File
Scatter - mito x UMIs #main/Scatter - mito x UMIs n/a
  • File
Scatter - mito x genes #main/Scatter - mito x genes n/a
  • File
Use_me_FVG #main/Use_me_FVG n/a
  • File
Use_me_Scaled #main/Use_me_Scaled n/a
  • File
Violin - Filterbycounts #main/Violin - Filterbycounts n/a
  • File
Violin - Filterbygenes #main/Violin - Filterbygenes n/a
  • File
Violin - Filterbymito #main/Violin - Filterbymito n/a
  • File
Violin - batch - log #main/Violin - batch - log n/a
  • File
Violin - genotype - log #main/Violin - genotype - log n/a
  • File
Violin - sex - log #main/Violin - sex - log n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_17 #main/_anonymous_output_17 n/a
  • File
_anonymous_output_18 #main/_anonymous_output_18 n/a
  • File
_anonymous_output_19 #main/_anonymous_output_19 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_20 #main/_anonymous_output_20 n/a
  • File
_anonymous_output_21 #main/_anonymous_output_21 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

1 (earliest) Created 22nd Apr 2024 at 11:20 by Helena Rasche

Added/updated 3 files


Open master a37fd01
help Creators and Submitter
Creators
  • Wendi Bacon
  • Julia Jakiela
Submitter
Tool
SCANPY
License
Creative Commons Attribution 4.0 International
Activity

Views: 28

Created: 22nd Apr 2024 at 11:20

Last updated: 22nd Apr 2024 at 11:20

help Attributions

None

Total size: 70.1 KB
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