Training for the bioconductor-scp tool #5709
Conversation
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@KristinaGomoryova ready to review? |
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There is also a single-cell topic. We currently have tutorials around scRNA-seq and scATAC-seq analysis in that topic. Do you think this tuitorial fits better there covering an additional modality in single-cell? |
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@shiltemann is there a way to symlink this tutorial also in the single-cell topic? |
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How cool! This is so exciting! |
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Thanks @KristinaGomoryova for the training and @pavanvidem for the review! @PratikDJagtap or @supernord do you know somebody else who could maybe also review this? |
Yes please, will be happy for feedback! :) |
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@KristinaGomoryova @hechth for me it is a bit confusing to see multiple hands-on boxes for a single tool run. It would be nice to have them as something like params box at each step and a final hands-on box with all the params together. For example, when testing, I clicked on the Run Tool button as soon as I filled first Hands-on box because this is the normal procedure. At least, there should be a warning box at the end of the first hands-on indicating not to run the tool and more parameters need to be set before running. |
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@pavanvidem could you provide an example of what you mean? |
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I mean some warning box like this after the first scp hands-on step would help. While I was testing the workflow, I pressed the "Run Tool" after the first hands-on and obviously got an error. |
| ## Data export | ||
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| In the end of the workflow, several datasets are exported. By default, a log transformed, normalized, imputed and batch-corrected data on the protein level are provided. Additionally, it is possible to export also intermediate results, meaning peptides, normalized peptides, log transformed peptides, proteins, normalized proteins and imputed proteins. Also, it is possible to export the scp object as an Rdata object, which can be further loaded into the R environment using the R load() function, and the Rscript to reproduce the analysis outside of Galaxy. Both plots and intermediate results will be provided as collections. | ||
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Please write a bit about the results and those beautiful plots :)
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thanks @pavanvidem |
This is the PR for the Galaxy training for bioconductor-scp tool, which allows the analysis of single-cell proteomics data. The input dataset (corresponding to input for the scp vignette) is on Zenodo; the workflow comprises only this one tool. Setting individual parameters is described extensively.
TODO: sort out how to refer the
Grouptool (which is not on the ToolShed, related issue here).