AnnData to Cell Data Set (CDS) conversion
Visit source
Download RO-CrateAnnData to CDS format conversion (manually using Galaxy buttons). This workflow does not include renaming the column containing gene symbols.
Associated Tutorial
This workflows is part of the tutorial AnnData to Cell Data Set (CDS) conversion, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Julia Jakiela, Morgan Howells, Wendi Bacon
Tutorial Contributor(s): Helena Rasche, Pavankumar Videm, Mehmet Tekman
Workflow Author(s): Julia Jakiela
Funder(s): ELIXIR-UK: FAIR Data Stewardship training
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AnnData | AnnData | Input file in AnnData format |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 2 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 3 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 4 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1 |
| 5 | Monocle3 create | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Inspect AnnData: obs | Inspect AnnData: obs | n/a |
|
| Inspect AnnData: var | Inspect AnnData: var | n/a |
|
| Inspect AnnData: X | Inspect AnnData: X | n/a |
|
| CDS Monocle file | CDS Monocle file | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:11 by Helena Rasche
Added/updated 4 files
Open
master39af45e
3.0 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche
Added/updated 4 files
Frozen
3.03cfd20f
Creators and Submitter
Views: 222 Downloads: 86
Created: 25th Jun 2024 at 11:15
Last updated: 25th Jun 2024 at 11:15
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
Web page: Not specified
Space: General
Public web page: https://galaxy.training
