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Hello,
I previously left a comment about having issues with arrow bias in the deicode biplot (scher-lab #56). The recommendation was to re-install with the dev version, which I did. However, re-ins…
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We are trying to implement proBatch into our data analysis pipelines, but our data has a lot of NAs. We've found that batch correction only works when we filter out peptides containing NAs which leav…
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Hi, I am using your package on Visium data as described in your recent manual, it works very fine! Related to that, I am wondering if there is a way to pull out identities of spots that have a particu…
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Hi Shuangbin,
I'm wondering how to set the aesthetic mapping of PCoA use the _mapping_ parameter in the _ggordpoint_ function. It seems to be that I can change the shape, size, or alpha of the p…
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Hello,
I have some methlyation EPICv2 data that I am trying to perform differential methylation regional (DMR) analysis on, and am having some trouble using the customized packages (specifically t…
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### Description
I didin't find the way of find the sample and variable scores or the biplot
### Purpose
The biplot represents the points in the dimension reduced space (principal components)
### U…
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Enhance the preprocessing module to handle a wider range of data types and transformations.
- Implement advanced categorical encoding techniques (e.g., target encoding, weight of evidence)
- Add o…
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When trying to run fastReport I noticed, that the ID for PCA and MDS Reports are the same. I believe that those functions (for pca `prcomp()` and for mds `cmdscale()` but also `isoMDS` and maybe the o…
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I first estimated rho, gene conversion rate and track lengths using mlrho and following the method in Lynch et al (2014; Genetics) from my data consisted of 20 unphased diploid individuals (40 chromso…
melop updated
2 years ago
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Hello! Thank you so much for this package. I would like to run svds using the BPCells wrapper function on a matrix containing 9,096 genes and 4,188,533 cells. I followed the workflow outlined in the v…