Workflow Type: Galaxy

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

Inputs

ID Name Description Type
AnnData - Loaded AnnData - Loaded n/a
  • File
MaxMTpc MaxMTpc Cells with more than this percentage of counts coming from mitochondrial genes will be removed.
  • float?
MinCountPerCell MinCountPerCell Cells with fewer than this number of total counts will be removed.
  • float?
MinGenesPerCell MinGenesPerCell Cells with fewer than this many distinct genes observed will be removed.
  • float?
Mitochondrial Prefix 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/1.8.1+1+galaxy1
6 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1
7 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1
8 Cell Filtering toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+1+galaxy0
9 Scanpy Scrublet toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_multiplet_scrublet/scanpy_multiplet_scrublet/1.8.1+1+galaxy0
10 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1

Outputs

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

Version History

main @ a95a4ee (latest) 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
Activity

Views: 2146

Created: 5th May 2023 at 07:49

Last updated: 9th Nov 2023 at 03:49

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