Add dsb component #588
Add dsb component #588
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| namespace: protein_processing | ||
| description: "Filter background and foreground signals for normalising protein expression with DSB (Denoised and Scaled by Background)." | ||
| authors: | ||
| - name: Xichen Wu |
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Use the author yaml to insert author information
| - name: Xichen Wu | |
| - __merge__: /src/authors/xichen_wu.yaml | |
| roles: [ maintainer, author ] |
| namespace: protein_processing | ||
| description: "Normalize protein expression with DSB (Denoised and Scaled by Background)." | ||
| authors: | ||
| - name: Xichen Wu |
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Use the author yaml to insert author information
| - name: Xichen Wu | |
| - __merge__: /src/authors/xichen_wu.yaml | |
| roles: [ maintainer, author ] |
| - name: "--data_raw" | ||
| type: file | ||
| required: true | ||
| description: "A ``MuData`` object containing raw (unfiltered, including empty droplets) data for both ``prot`` and ``rna`` modalities." |
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We typically use --input to denote an input mudata object in openpipelines
| - name: "--data_raw" | |
| type: file | |
| required: true | |
| description: "A ``MuData`` object containing raw (unfiltered, including empty droplets) data for both ``prot`` and ``rna`` modalities." | |
| - name: "--input" | |
| type: file | |
| required: true | |
| description: "A ``MuData`` object containing raw (unfiltered, including empty droplets) data for both ``prot`` and ``rna`` modalities." | |
| example: input.h5mu |
| type: file | ||
| direction: output | ||
| description: dsb_index output directory | ||
| example: "dsb_output" |
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Make this a required argument and add a slash to the example to denote it's a directory
| example: "dsb_output" | |
| example: "dsb_output/" | |
| required: true |
| multiple: true | ||
| - name: "--output" | ||
| type: file | ||
| direction: output |
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I'd be inclined to make the output an h5mu file instead of a directory, because then it plays much nicer with the other components in OpenPipeline. If you want, we can discuss this in the next OpenPipelines working meeting.
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Hi @wxicu ! Just following up on this PR. Do you have any thoughts about the comments I placed? |
Hey really sorry for my late response. Finally have time now to contribute on this. I will go through all the comments and update it soon! Again, really sorry for the delay |
Changelog
Add dsb component: which splits the dsb function into two components, the first takes care of recognising the barcodes for foreground and the background, while the second does the actual normalization
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Proposed changes are described in the CHANGELOG.md
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