AnnData object to Monocle input files
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/875?version=1

Inputs

ID Name Description Type
AnnData before processing to extract clean expression matrix #main/AnnData before processing to extract clean expression matrix n/a
  • File
AnnData to extract genes & cells annotations #main/AnnData to extract genes & cells annotations n/a
  • File

Steps

ID Name Description
2 Extract cell annotations toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
3 Extract gene annotations toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
4 Extract clean expression matrix Unprocessed means here before normalisation or dimensionality reduction. For this step, must have cell IDs as rownames. toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
5 Filter out unwanted cell types Double-check the cell_type column number Filter1
6 gene_short_name annotation Check the number of the column with genes names (using column) and its header (Find Regex) toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.2
7 Cut cells IDs Cut1
8 Cut genes IDs Cut1
9 Filter matrix (by cells) join1
10 Remove duplicate column (cells IDs) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0
11 Transpose matrix toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2
12 Filter matrix (by genes) join1
13 Remove duplicate column (genes IDs) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0

Outputs

ID Name Description Type
Cells without macrophages #main/Cells without macrophages n/a
  • File
Extracted cell annotations (obs) #main/Extracted cell annotations (obs) n/a
  • File
Extracted gene annotations (var) #main/Extracted gene annotations (var) n/a
  • File
Filtered cells IDs #main/Filtered cells IDs n/a
  • File
Filtered matrix (by cells & genes) #main/Filtered matrix (by cells & genes) n/a
  • File
Filtered matrix (by cells) #main/Filtered matrix (by cells) n/a
  • File
Genes IDs #main/Genes IDs n/a
  • File
Genes table with gene_short_name colname #main/Genes table with gene_short_name colname n/a
  • File
Pre-filtered matrix (by cells & genes) #main/Pre-filtered matrix (by cells & genes) n/a
  • File
Pre-filtered matrix (by cells) #main/Pre-filtered matrix (by cells) n/a
  • File
Unprocessed expression matrix #main/Unprocessed expression matrix n/a
  • File
filtered matrix (by cells) transposed #main/filtered matrix (by cells) transposed n/a
  • File

Version History

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

Added/updated 3 files


Open master a708957
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License
Creative Commons Attribution 4.0 International
Activity

Views: 57

Created: 22nd Apr 2024 at 10:40

Last updated: 22nd Apr 2024 at 10:41

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Total size: 30.3 KB
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