NCBI to Anndata 2.0
Visit source
Download RO-Crate
Run on GalaxyAssociated Tutorial
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: 1149 Downloads: 177 Runs: 0
Created: 2nd Jun 2025 at 10:58
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
