Load example package data | log transform | dsb step 1 removal of ambient noise | dsb step II Part I fitting single cell models to extract background | dsb Part II step II | How can I interpret the dsb values?

Table of Contents | Background and motivation | Installation and quick overview | Download public 10X Genomics data | Step 1 A note on alignment of ADTs | Step 2 Load RNA and ADT data and define droplet quality control metadata | Step 3 Quality control cells and background droplets | Optional step; remove proteins without staining | Step 4 Normalize protein data with the DSBNormalizeProtein Function | Integrating dsb with Seurat | Clustering cells based on dsb normalized protein using Seurat | dsb derived cluster interpretation | Weighted Nearest Neighbor multimodal clustering using dsb normalized values with Seurat | Method 1 -- Seurat WNN default with PCA on dsb normalized protein | Method 2-- Seurat WNN with dsb normalized protein directly without PCA | Some recent publications using dsb | using other alignment algorithms | A note on Cell Ranger --expect-cells

Integrating dsb with Bioconductor | Using dsb in Python | Using dsb with data lacking isotype controls | Using dsb with sample multiplexing experiments | Advanced usage - return internal stats used by dsb | outlier clipping with the quantile.clipping argument | Using a different background scaling method | Frequently Asked Questions | check for outliers in dsb normalized values

To Run The Main HDStIM Function | Output | To Plot Diagnostic Figures | Plots Explaining K-means Clustering And Fisher's Exact Test | UMAP Plots To Visually Inspect Responding and Non-Responding Cell Mapping | Distribution Plots for Individual State Marker before And After Mapping | To Rank State/Signaling Markers According To Their Contribution To The Response