Cell Cycle Regression Workflow
Visit source
Download RO-CrateAssociated Tutorial
This workflows is part of the tutorial Removing the effects of the cell cycle, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Marisa Loach
Tutorial Author(s): Marisa Loach
Tutorial Contributor(s): Wendi Bacon, Graeme Tyson, Pavankumar Videm, Helena Rasche, Marisa Loach, Saskia Hiltemann, Julia Jakiela, Mehmet Tekman
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
2.0 (latest) Created 20th Jan 2025 at 13:06 by Helena Rasche
Added/updated 4 files
Open
masterfb804ae
1.0 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche
Added/updated 4 files
Frozen
1.02b462b8
Creators and Submitter
Views: 456 Downloads: 110
Created: 25th Jun 2024 at 11:15
Last updated: 20th Jan 2025 at 13:06
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
