Workflow Type: Galaxy
Updated 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

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Views: 40 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:57

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