Workflow Type: Galaxy
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Stable
Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.
Inputs
ID | Name | Description | Type |
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AnnData - Loaded | #main/AnnData - Loaded | n/a |
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MaxMTpc | #main/MaxMTpc | Cells with more than this percentage of counts coming from mitochondrial genes will be removed. |
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MinCountPerCell | #main/MinCountPerCell | Cells with fewer than this number of total counts will be removed. |
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MinGenesPerCell | #main/MinGenesPerCell | Cells with fewer than this many distinct genes observed will be removed. |
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Mitochondrial Prefix | #main/Mitochondrial Prefix | Prefix on mitochondrial gene names. Default MT- typical for human, mt- for mouse. If mitochondrial genes are not prefixed, Mito flagging, plotting and filtering steps will need to be removed. |
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Steps
ID | Name | Description |
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5 | Flag Mt- genes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
6 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy2 |
7 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy2 |
8 | Cell Filtering | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.9.3+galaxy0 |
9 | Scanpy Scrublet | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_multiplet_scrublet/scanpy_multiplet_scrublet/1.9.3+galaxy0 |
10 | Plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy2 |
Outputs
ID | Name | Description | Type |
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genecount_qc_plot | #main/genecount_qc_plot | n/a |
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mito_qc_plot | #main/mito_qc_plot | n/a |
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qc_anndata_object | #main/qc_anndata_object | n/a |
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top_genes_plot | #main/top_genes_plot | n/a |
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Version History
main @ 7581788 (latest) Created 30th May 2024 at 06:51 by Sarah Williams
Updated workflow versions for anndata version conflict bugfix
Frozen
main
7581788
main @ a95a4ee Created 22nd Jun 2023 at 07:28 by Sarah Williams
counts matrix workflow doc, affiliations
Frozen
main
a95a4ee
main @ a95a4ee Created 21st Jun 2023 at 07:48 by Sarah Williams
counts matrix workflow doc, affiliations
Frozen
main
a95a4ee
master @ 76f52ed (earliest) Created 5th May 2023 at 07:49 by Sarah Williams
count and load
Frozen
master
76f52ed
Creators and Submitter
Creators
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Tool
Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
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Views: 5016 Downloads: 621 Runs: 0
Created: 5th May 2023 at 07:49
Last updated: 30th May 2024 at 06:51
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