Cell Cycle Regression Workflow
1.0

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Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Cell Cycle Regression Workflow, available in the GTN

Thanks to...

Tutorial Author(s): Marisa Loach

Tutorial Contributor(s): Wendi Bacon, Graeme Tyson

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1246?version=1

Inputs

ID Name Description Type
AnnData (After QC, normalisation, scaling) #main/AnnData (After QC, normalisation, scaling) n/a
  • File
G2M Phase Genes #main/G2M Phase Genes n/a
  • File
Pasted Entry #main/Pasted Entry n/a
  • File
S Phase Genes #main/S Phase Genes n/a
  • File

Steps

ID Name Description
4 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
5 All Cell Cycle Genes (Concatenate S and G2M Genes) cat1
6 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0
7 Table Compute toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
8 Add column toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0
9 Scanpy RegressOut toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0
10 Add column toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0
11 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
12 Sort sort1
13 Table Compute toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
14 Concatenate datasets cat1
15 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
16 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
17 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
18 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
19 Cluster, infer trajectories and embed toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0
20 Cluster, infer trajectories and embed toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0
21 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1
22 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1

Outputs

ID Name Description Type
Cluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix #main/Cluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix n/a
  • File
Scanpy RegressOut on input dataset(s): Regressed out AnnData #main/Scanpy RegressOut on input dataset(s): Regressed out AnnData 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
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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
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 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
  • 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 11:15 by Helena Rasche

Added/updated 4 files


Open master 2b462b8
help Creators and Submitter
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GTN Matrix
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SCANPY
License
Creative Commons Attribution 4.0 International
Activity

Views: 394   Downloads: 97

Created: 25th Jun 2024 at 11:15

Last updated: 25th Jun 2024 at 11:15

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