New Evaluating Reference Data for Bulk RNA Deconvolution tutorial #5549
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…m/hexhowells/training-material into deconvolution-evaluation-tutorial
…m/hexhowells/training-material into deconvolution-evaluation-tutorial
…m/hexhowells/training-material into deconvolution-evaluation-tutorial
…m/hexhowells/training-material into deconvolution-evaluation-tutorial
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Thanks @hexhowells! This looks great. A few minor comment below. And I can't speak to the science, but perhaps @nomadscientist can have a look here as well?
| title: Evaluating Reference Data for Bulk RNA Deconvolution | ||
| subtopic: deconvo | ||
| priority: 3 | ||
| zenodo_link: '' |
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| zenodo_link: '' | |
| zenodo_link: 'https://zenodo.org/records/5719228' |
| > - *"Delimited by"*: `Tab` | ||
| > - *"How should the results be sorted?"*: `With the most common value first` | ||
| > | ||
| > 2. **Rename** {% icon galaxy-pencil %} output `Cell type counts` |
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maybe add the faq for renaming a dataset here at the first time people are asked to do it?
| > {% snippet faqs/galaxy/workflows_run.md %} | ||
| {: .hands_on} | ||
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| <iframe title="Galaxy Workflow Embed" style="width: 100%; height: 700px; border: none;" src="https://usegalaxy.eu/published/workflow?id=76d3408d0d22ad05&embed=true&buttons=true&about=false&heading=false&minimap=true&zoom_controls=true&initialX=-20&initialY=-20&zoom=0.5"></iframe> |
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| title: Evaluating Reference Data for Bulk RNA Deconvolution | ||
| subtopic: deconvo | ||
| priority: 3 |
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did you mean for this tutorial to be 3rd in the subsection? It is second now because the other tutorials in the subsections have priorities 1 and 4 listed. So please double check if the order is how you want it now.
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| **Remember** since we have a collection of 20 inputs, the output of this workflow will be a collection of 20 elements, each corresponding to the input elements. Each output will have its own random selection of 200 cells. | ||
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| > <comment-title>Inputting multiple datasets</comment-title> |
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this could probably be an FAQ. or maybe you could use the existing "select multiple datasets" faq ? And maybe enhance it with your screenshot?
| > - Copy the URL (e.g. via right-click) of [this workflow](https://usegalaxy.eu/u/hexhowells/w/deconv-eval-stage-1) or download it to your computer. | ||
| > - Import the workflow into Galaxy | ||
| > | ||
| > {% snippet faqs/galaxy/workflows_run_trs.md path="topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.ga" title="QC Report" %} |
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this is a tad confusing, as it is a hands-on box within a hands-on box. Are they meant to run this QC report workflow at this point? Or did you mean to replace the workflow with the one mentioned in step 1 here?
| > <hands-on-title>Run pseudo-bulk and actual proportions workflow</hands-on-title> | ||
| > | ||
| > 1. **Import the workflow** into Galaxy | ||
| > - Copy the URL (e.g. via right-click) of [this workflow](https://usegalaxy.eu/u/hexhowells/w/deconv-eval-stage-1) or download it to your computer. |
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please include the workflow here in the GTN as well and refer to that in the link.
| > - {% icon param-file %} *"Input Dataset"*: `Transposed expression matrix` | ||
| > - *"Size of output collection"*: `20` | ||
| > | ||
| > 4. **Rename** {% icon galaxy-pencil %} output `Expression data` |
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I would recommend thinking about keeping the terms consistent, as later on when the first workflow is run, these inputs are described with different terminology
| > In order to upload the input collections into the workflow, you first need to set the input type to **Multiple datasets** in the input file selection. | ||
| > | ||
| >  | ||
| {: .comment} |
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I experienced some difficulty loading these collections into the workflow. They would not appear in the pull down menu, and I had to drag and drop the collections without visual confirmation that they had been uploaded.
| > - {% icon param-collection %} *"Expression Data"*: `Expression Data` | ||
| > | ||
| > {% snippet faqs/galaxy/workflows_run.md %} | ||
| > 3. Add a tag labelled `#A` to the first "Actual cell proportions" and "Pseudobulk" collections |
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I am not completely sure, but I feel like the term "actual cell proportions" might be a little misleading. The cell proportions, as indicated by proportional representation in the single-cell data, are often different from the true in vivo cell type proportions due to systematic drop out biases during data collection. This might be worth mentioning, or maybe a different term which doesn't use "actual" could be substituted.
| > {% snippet faqs/galaxy/workflows_run_trs.md path="topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.ga" title="QC Report" %} | ||
| > | ||
| > 2. Run **Workflow inferring cellular proportions** {% icon workflow %} using the following parameters: | ||
| > - {% icon param-collection %} *"Pseudobulk - A"*: `expression data - A` |
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These collections also did not appear in the drop down menus, and rather had to be dragged and dropped.
| > > | ||
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| > > 1. Comparing scatter plots, the MuSiC tool has the most accurate results since the points fall closer onto the x=y line |
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Imagine the case that the NNLS deconvolution more closely resembled the cell proportions in the real, biological context, while MuSic more accurately recapitulated with proportions from the single cell data. Which if these two methods are really more accurate, then?
New tutorial on evaluating reference data for bulk RNA deconvolution tools, evaluating both MuSiC and NNLS deconvolution tools within Galaxy.