Workflow Type: Galaxy
Frozen
Frozen
Frozen
Frozen
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 |
|
MaxMTpc | MaxMTpc | Cells with more than this percentage of counts coming from mitochondrial genes will be removed. |
|
MinCountPerCell | MinCountPerCell | Cells with fewer than this number of total counts will be removed. |
|
MinGenesPerCell | MinGenesPerCell | Cells with fewer than this many distinct genes observed will be removed. |
|
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. |
|
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 |
|
mito_qc_plot | mito_qc_plot | n/a |
|
qc_anndata_object | qc_anndata_object | n/a |
|
top_genes_plot | top_genes_plot | n/a |
|
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
Submitter
Tool
Activity
Views: 4579 Downloads: 555 Runs: 0
Created: 5th May 2023 at 07:49
Last updated: 30th May 2024 at 06:51
Annotated Properties
Tags
Attributions
None
Collections