Monocle3 workflow
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/876?version=1

Inputs

ID Name Description Type
Cell annotations input #main/Cell annotations input n/a
  • File
Expression matrix input #main/Expression matrix input n/a
  • File
Gene annotations input #main/Gene annotations input n/a
  • File

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
  • File
Cell type plot #main/Cell type plot n/a
  • File
Cell types & learned trajectory path plot #main/Cell types & learned trajectory path plot n/a
  • File
Cluster plot #main/Cluster plot n/a
  • File
Differential expression of genes - table #main/Differential expression of genes - table n/a
  • File
Gene expression plot #main/Gene expression plot n/a
  • File
Genotype plot #main/Genotype plot n/a
  • File
Monocle3 create on input dataset(s): cds3 #main/Monocle3 create on input dataset(s): cds3 n/a
  • File
Monocle3 learnGraph on input dataset(s): cds3 #main/Monocle3 learnGraph on input dataset(s): cds3 n/a
  • File
Monocle3 orderCells on input dataset(s): cds3 #main/Monocle3 orderCells on input dataset(s): cds3 n/a
  • File
Monocle3 partition on input dataset(s): cds3 #main/Monocle3 partition on input dataset(s): cds3 n/a
  • File
Monocle3 preprocess on input dataset(s): cds3 #main/Monocle3 preprocess on input dataset(s): cds3 n/a
  • File
Monocle3 reduceDim on input dataset(s): cds3 #main/Monocle3 reduceDim on input dataset(s): cds3 n/a
  • File
Partition plot #main/Partition plot n/a
  • File
Pseudotime plot #main/Pseudotime plot n/a
  • File
Sex plot #main/Sex plot n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File

Version History

1 (earliest) Created 22nd Apr 2024 at 10:41 by Helena Rasche

Added/updated 3 files


Open master b31676a
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Created: 22nd Apr 2024 at 10:41

Last updated: 22nd Apr 2024 at 10:41

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