NCBI to Anndata 2.0
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This workflows is part of the tutorial Converting NCBI Data to the AnnData Format, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Morgan Howells, Pavankumar Videm
Tutorial Author(s): Morgan Howells
Tutorial Contributor(s): Wendi Bacon, Pavankumar Videm, Mehmet Tekman, Helena Rasche, Morgan Howells, Saskia Hiltemann, Pablo Moreno, Julia Jakiela, Björn Grüning
Grants(s): DASH UK
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GSM5353214_PA_AUG_PB_1A_S1_dge.txt | GSM5353214_PA_AUG_PB_1A_S1_dge.txt | n/a |
|
| GSM5353215_PA_AUG_PB_1B_S2_dge.txt | GSM5353215_PA_AUG_PB_1B_S2_dge.txt | n/a |
|
| GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt | GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt | n/a |
|
| GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt | GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt | n/a |
|
| GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt | GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt | n/a |
|
| GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt | GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt | n/a |
|
| GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt | GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt | n/a |
|
| GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt | GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt | n/a |
|
| GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt | GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt | n/a |
|
| GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt | GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 11 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 12 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 13 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 14 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 15 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 16 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 17 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 18 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 19 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 20 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 21 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 22 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 23 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 24 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 25 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 26 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 27 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 28 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 29 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 30 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 31 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 32 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 33 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 34 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 35 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 36 | Cut | Cut1 |
| 37 | Cut | Cut1 |
| 38 | Cut | Cut1 |
| 39 | Cut | Cut1 |
| 40 | Paste | Paste1 |
| 41 | Paste | Paste1 |
| 42 | Paste | Paste1 |
| 43 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 44 | Scanpy FilterCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.9.3+galaxy0 |
| 45 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
| 46 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output_h5ad | output_h5ad | n/a |
|
| obs | obs | n/a |
|
Version History
master
Creators and Submitter
Views: 50 Downloads: 7 Runs: 0
Created: 2nd Jun 2025 at 10:58
AttributionsNone
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