Pseudobulk: Suggestions of genes to ignore per contrast field

[pcm32]

Description

While EdgeR and Decoupler try to filter out genes that are lowly expressed, for experiments with many contrasts it can often happens that only some contrasts will have a low count for certain genes (but since in other contrasts they are high, the gene shouldn't be filtered out across the board). This is an attempt at flagging those very lowly expressed genes per contrast field (so that they can be filtered out of complete contrasts down the pipeline, after DE, before GSEA, etc).

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Checklist

• I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
• If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
• If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).
• If I changed the version, the @TOOL_VERSION@ part of the version does not contain any + symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only + should be the one preceding galaxy<build> (unless that all the versions from that tool previously followed a different pattern).