AnnData object to Monocle input files
1.0

Workflow Type: Galaxy

Preparing and filtering gene and cell annotations files and expression matrix to be passed as input for Monocle

Associated Tutorial

This workflows is part of the tutorial AnnData object to Monocle input files, 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

gtn star logo followed by the word workflows

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

1.0 (earliest) Created 25th Jun 2024 at 11:13 by Helena Rasche

Added/updated 4 files


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Views: 327   Downloads: 69

Created: 25th Jun 2024 at 11:13

Last updated: 25th Jun 2024 at 11:13

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