Scanpy FilterGenes (version 1.9.3+galaxy0)

Input object in AnnData/Loom format:

Format of input object:

Format of output object:

AnnData or Loom. Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.

Parameters to select genes to keeps

Parameters to select genes to keep 0

Categories to select genes to keep (unless negate is checked)s

Categories to select genes to keep (unless negate is checked) 0

Subsets to select genes to keeps

Subsets to select genes to keep 0

Force recalculation of QC vars:

If set, it will recalculate pcts and other existing QC vars, overwriting existing ones.

Save adata to adata.raw before processing?:

Save adata.X to the specified layer before processing.:

Save to 10x mtx format:

If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format.

Filter genes based on arbitrary attributes (scanpy.pp.filter_genes)

Keep genes that have at least min_counts counts or are expressed in at least min_cells cells or have at most max_counts counts or are expressed in at most max_cells cells. Other gene attributes can be used for filtering too if available.

More information can be found at https://scanpy.readthedocs.io

Version history 1.9.301+galaxy0: Moves to Scanpy 1.9.3

1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations, adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.

1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.

1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.

1.8.1+1+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.

1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.

1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.

1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/

1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.

1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.

1.4.3+galaxy10: Use profile 18.01 for modules.

1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.

1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).

1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).

1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.

1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.