scp
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UCLouvain-CBIO
Single cell proteomics data processing
This issue is to keep track of the progress of the unit testing. Unit test should be written for the function in the following scripts: - [x] `R/ScpModel-Class.R` - [x]...
We should explicitly document in the vignette how to make additional useful visualisation. Current ideas: ## Intensity plot Show peptide/protein intensities vs other covariates. Eg (from [scplainer article](https://github.com/UCLouvain-CBIO/2023-scplainer/blob/13726cd3e76de008be92b996e65991e1ef2d3111/3_make_figures/make_figure2.R#L101C1-L116C25)):  Code...
The issues has been highlighted in: https://github.com/UCLouvain-CBIO/scp/issues/56#issuecomment-2010539916 The reason is that the subsetting functionality in `QFeatures` does not know it should also subset the `ScpModel` objects contained in `metadata(qfObject)`. A...
Hello, I am trying the scplainer workflow on my own data. I noticed that when using scpVolcanoPlot() to create a volcano plot, the group order provided to scpDifferentialAnalysis() is not...
Cite the new [scp workflow](https://arxiv.org/abs/2310.13598) in the vignette.
As requested by the Slavov lab. A concern for new users is 'will my data work with scp'? Lower that barrier is essential! GUIs can be a good way to...
Let's have a function that computes a metric or statistic for every cell across several batches. The function would be a generalization of `computeMedianCVperCell()`. *Tentative signature*: `computePerCell(object, i, colDataName, FUN,...
I have done some edits. In addition, here are some comments: 1. Explain why counting during aggregation, if there's any reason. 2. Wouldn't a function to create the peptide identification...
(The current issue is more of a food for thought than an actual issue. Still, I think our package could clarify the concept of coefficient of variation (CV) a bit...
I think we should consider several improvements: 1. `divideByReference()` is a type of normalization (normalization by reference channel), therefore I think it should be made accessible from `normalizeSCP()`. This means...