Combining datasets after pre-processing 1.0
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Run on GalaxyUpdated March 2024
Associated Tutorial
This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN
Thanks to...
Workflow Author(s): Julia Jakiela, Wendi Bacon
Tutorial Author(s): Wendi Bacon
Tutorial Contributor(s): Helena Rasche, Jonathan Manning, Julia Jakiela, Pavankumar Videm, Saskia Hiltemann, Björn Grüning, Marisa Loach, Wendi Bacon, Bérénice Batut, Mehmet Tekman, Pablo Moreno
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| N701 | N701 | Dataset to be combined |
|
| N702 | N702 | Dataset to be combined |
|
| N703 | N703 | Dataset to be combined |
|
| N704 | N704 | Dataset to be combined |
|
| N705 | N705 | Dataset to be combined |
|
| N706 | N706 | Dataset to be combined |
|
| N707 | N707 | Dataset to be combined |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Concatenating Datasets | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 8 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 9 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 10 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 11 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0 |
| 12 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0 |
| 13 | Cut | Cut1 |
| 14 | Cut | Cut1 |
| 15 | Paste | Paste1 |
| 16 | Adding in cell metadata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 17 | Batching Cell Metadata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 18 | Calculating mitochondrial | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Combined Object | Combined Object | n/a |
|
| Sex metadata | Sex metadata | n/a |
|
| Genotype metadata | Genotype metadata | n/a |
|
| Cell metadata | Cell metadata | n/a |
|
| AnnData with Cell Metadata | AnnData with Cell Metadata | n/a |
|
| Batched Object | Batched Object | n/a |
|
| Annotated AnnData | Annotated AnnData | n/a |
|
Version History
master
Creators and Submitter
Views: 244 Downloads: 34 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
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