Filter, Plot and Explore Single-cell RNA-seq Data updated
1.0

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Workflow Type: Galaxy

Filter, Plot and Explore Single-cell RNA-seq Data

Associated Tutorial

This workflows is part of the tutorial Filter, Plot and Explore Single-cell RNA-seq Data updated, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): Wendi Bacon

Tutorial Contributor(s): Helena Rasche, Julia Jakiela

Workflow Author(s): Wendi Bacon, Julia Jakiela

SEEK ID: https://dev.workflowhub.eu/workflows/1212?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

1.0 (earliest) Created 25th Jun 2024 at 11:11 by Helena Rasche

Added/updated 4 files

Open master 96d4416

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

Tool

SCANPY

License

Creative Commons Attribution 4.0 International

Activity

Views: 431 Downloads: 105

Created: 25th Jun 2024 at 11:11

Last updated: 25th Jun 2024 at 11:11

Filter, Plot and Explore Single-cell RNA-seq Data updated 1.0