This small pull request updates the HTO Skript and makes it more stable for production. The changes are mostly cosmetic. Most importantly normalisation for UMAP is now done with Seurat's standard LogNormalize approach. This is followed by UMAP for visualisation. Standard clustering is done as well and includes doublets and negatives. Distribution of cells in clusters for each individual HTO+negatives/doublets (and vice versa) as well as QC (counts, features) parameters for each cluster and HTO+negatives/doublets are very informative for cell quality and could be included in filtering later on.
IMPORTANT: Please do the PR only once the other PR for the DEGs is done. There are some minor changes which also apply to the main script.
This small pull request updates the HTO Skript and makes it more stable for production. The changes are mostly cosmetic. Most importantly normalisation for UMAP is now done with Seurat's standard LogNormalize approach. This is followed by UMAP for visualisation. Standard clustering is done as well and includes doublets and negatives. Distribution of cells in clusters for each individual HTO+negatives/doublets (and vice versa) as well as QC (counts, features) parameters for each cluster and HTO+negatives/doublets are very informative for cell quality and could be included in filtering later on.
IMPORTANT: Please do the PR only once the other PR for the DEGs is done. There are some minor changes which also apply to the main script.