NCBI to Anndata
Visit source
Download RO-CrateAssociated Tutorial
This workflows is part of the tutorial NCBI to Anndata, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Morgan Howells
Tutorial Contributor(s): Wendi Bacon, Pavankumar Videm, Mehmet Tekman, Helena Rasche
Workflow Author(s): Morgan Howells, Pavankumar Videm
Funder(s): ELIXIR-UK: FAIR Data Stewardship training
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 and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 11 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 12 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 13 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 14 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 15 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 16 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 17 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 18 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 19 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 |
| 20 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 21 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 22 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 23 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 24 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 25 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 26 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 27 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 28 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 29 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 30 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 31 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 32 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 33 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 34 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 35 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 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/0.7.5+galaxy1 |
| 44 | Scanpy FilterCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9 |
| 45 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0 |
| 46 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output_h5ad | output_h5ad | n/a |
|
| obs | obs | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master9eb46a3
2.0 (earliest) Created 25th Jun 2024 at 11:18 by Helena Rasche
Added/updated 4 files
Frozen
2.0f188c63
Creators and Submitter
Views: 519 Downloads: 140
Created: 25th Jun 2024 at 11:18
Last updated: 25th Jun 2024 at 11:18
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
