LOCKED | Combining single cell datasets after pre-processing
1.0

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Workflow Type: Galaxy

Workflow associated with this training: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html

Associated Tutorial

This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN

Features

Thanks to...

Workflow Author(s): Wendi Bacon

Tutorial Author(s): Wendi Bacon

Tutorial Contributor(s): Helena Rasche, Jonathan Manning, Julia Jakiela, Pavankumar Videm, Saskia Hiltemann, Björn Grüning, Marisa Loach, Wendi Bacon, Bérénice Batut, Mehmet Tekman, Pablo Moreno

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SEEK ID: https://workflowhub.eu/workflows/1543?version=1

Inputs

ID Name Description Type
Sample 1 #main/Sample 1 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File
Sample 2 #main/Sample 2 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File
Sample 3 #main/Sample 3 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File
Sample 4 #main/Sample 4 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File
Sample 5 #main/Sample 5 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File
Sample 6 #main/Sample 6 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File
Sample 7 #main/Sample 7 The training uses 7 different AnnData objects. This is 1 of them. The order does matter.
  • File

Steps

ID Name Description
7 Combined_Object toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1
8 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
9 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
10 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
11 Generating sex metadata toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0
12 Generating genotype metadata toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0
13 Sex_Metadata Cut1
14 Genotype_metadata Cut1
15 Cell_Metadata Paste1
16 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1
17 Batched_Object toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1
18 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1

Outputs

ID Name Description Type
Batched_Object #main/Batched_Object n/a
  • File
Cell_Metadata #main/Cell_Metadata n/a
  • File
Combined_Object #main/Combined_Object n/a
  • File
Genotype_metadata #main/Genotype_metadata n/a
  • File
Sex_Metadata #main/Sex_Metadata n/a
  • File
anndata #main/anndata n/a
  • File
general #main/general n/a
  • File
obs #main/obs n/a
  • File
obs-final #main/obs-final n/a
  • File
outfile #main/outfile n/a
  • File
outfile-genotype #main/outfile-genotype n/a
  • File
var #main/var n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:58 by GTN Bot

Added/updated 4 files


Open master 9d1c350
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tool
anndata
License
MIT License (MIT)
Activity

Views: 2194   Downloads: 296   Runs: 0

Created: 2nd Jun 2025 at 10:57

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Total size: 191 KB
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