Workflow Type: Galaxy
Stable

Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.

Inputs

ID Name Description Type
AnnData - Loaded #main/AnnData - Loaded n/a
  • File
MaxMTpc #main/MaxMTpc Cells with more than this percentage of counts coming from mitochondrial genes will be removed.
  • float
MinCountPerCell #main/MinCountPerCell Cells with fewer than this number of total counts will be removed.
  • float
MinGenesPerCell #main/MinGenesPerCell Cells with fewer than this many distinct genes observed will be removed.
  • float
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.
  • string

Steps

ID Name Description
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
genecount_qc_plot #main/genecount_qc_plot n/a
  • File
mito_qc_plot #main/mito_qc_plot n/a
  • File
qc_anndata_object #main/qc_anndata_object n/a
  • File
top_genes_plot #main/top_genes_plot n/a
  • File

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
help Creators and Submitter
Creators
  • Sarah Williams
  • Mike Thang
  • Valentine Murigneaux
Submitter
Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
License
Activity

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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Total size: 3.75 MB
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