Monocle3 workflow 1.0
Visit source
Download RO-CrateTrajectory analysis using Monocle3, starting from 3 input files: expression matrix, gene and cell annotations
Associated Tutorial
This workflows is part of the tutorial Monocle3 workflow, available in the GTN
Thanks to...
Tutorial Author(s): Julia Jakiela
Tutorial Contributor(s): Helena Rasche, Wendi Bacon
Funder(s): EPSRC Training Grant DTP 2020-2021 Open University
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cell annotations input | #main/Cell annotations input | n/a |
|
| Expression matrix input | #main/Expression matrix input | n/a |
|
| Gene annotations input | #main/Gene annotations input | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Monocle3 create | Check the data format that you're using. toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2 |
| 4 | Monocle3 preprocess | You might want to change the dimensionality of the reduced space here. toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0 |
| 5 | Monocle3 reduceDim | UMAP/tSNE/PCA/LSI. However for further steps you need to use UMAP. toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0 |
| 6 | Monocle3 partition | You might want to change resolution (affects clusters) and/or q-value (affects partitions). toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0 |
| 7 | Plot cell type | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 8 | Plot genotype | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 9 | Plot batch | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 10 | Plot sex | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 11 | Monocle3 top markers | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+galaxy0 |
| 12 | Plot genes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 13 | Plot partition | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 14 | Plot cluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 15 | Monocle3 learnGraph | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0 |
| 16 | Plot learned trajectory | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
| 17 | Monocle3 orderCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0 |
| 18 | Monocle3 diffExp | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1 |
| 19 | Plot pseudotime | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Batch plot | #main/Batch plot | n/a |
|
| Cell type plot | #main/Cell type plot | n/a |
|
| Cell types & learned trajectory path plot | #main/Cell types & learned trajectory path plot | n/a |
|
| Cluster plot | #main/Cluster plot | n/a |
|
| Differential expression of genes - table | #main/Differential expression of genes - table | n/a |
|
| Gene expression plot | #main/Gene expression plot | n/a |
|
| Genotype plot | #main/Genotype plot | n/a |
|
| Monocle3 create on input dataset(s): cds3 | #main/Monocle3 create on input dataset(s): cds3 | n/a |
|
| Monocle3 learnGraph on input dataset(s): cds3 | #main/Monocle3 learnGraph on input dataset(s): cds3 | n/a |
|
| Monocle3 orderCells on input dataset(s): cds3 | #main/Monocle3 orderCells on input dataset(s): cds3 | n/a |
|
| Monocle3 partition on input dataset(s): cds3 | #main/Monocle3 partition on input dataset(s): cds3 | n/a |
|
| Monocle3 preprocess on input dataset(s): cds3 | #main/Monocle3 preprocess on input dataset(s): cds3 | n/a |
|
| Monocle3 reduceDim on input dataset(s): cds3 | #main/Monocle3 reduceDim on input dataset(s): cds3 | n/a |
|
| Partition plot | #main/Partition plot | n/a |
|
| Pseudotime plot | #main/Pseudotime plot | n/a |
|
| Sex plot | #main/Sex plot | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
Version History
1.0 (earliest) Created 25th Jun 2024 at 11:14 by Helena Rasche
Added/updated 4 files
Open
masterb1955c0
Creators and Submitter
Views: 489 Downloads: 107
Created: 25th Jun 2024 at 11:14
Last updated: 25th Jun 2024 at 11:14
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
