Workflow Type: Galaxy
Open
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
Inputs
ID | Name | Description | Type |
---|---|---|---|
AnnData (After QC, normalisation, scaling) | #main/AnnData (After QC, normalisation, scaling) | n/a |
|
G2M Phase Genes | #main/G2M Phase Genes | n/a |
|
Pasted Entry | #main/Pasted Entry | n/a |
|
S Phase Genes | #main/S Phase Genes | n/a |
|
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 |
|
Scanpy RegressOut on input dataset(s): Regressed out AnnData | #main/Scanpy RegressOut on input dataset(s): Regressed out AnnData | n/a |
|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
_anonymous_output_12 | #main/_anonymous_output_12 | n/a |
|
_anonymous_output_13 | #main/_anonymous_output_13 | n/a |
|
_anonymous_output_14 | #main/_anonymous_output_14 | n/a |
|
_anonymous_output_15 | #main/_anonymous_output_15 | n/a |
|
_anonymous_output_16 | #main/_anonymous_output_16 | n/a |
|
_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
_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 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche
Added/updated 4 files
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Created: 25th Jun 2024 at 11:15
Last updated: 25th Jun 2024 at 11:15
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