Package: scDblFinder 1.27.5

tl;dr | Mathematical background | Normalization by library size | Testing for (lack of) intermediacy | Calling doublet clusters | Discussion | Session information

tl;dr | Algorithm overview | Size factor handling | Normalization size factors | RNA content size factors | Interactions between them | Doublet score calculations | Session information

Introduction | computeDoubletDensity | recoverDoublets | scDblFinder | directDblClassification | findDoubletClusters | Installation | Which method to choose? | Session information

Installation | Usage | Cluster-based approach | Multiple samples | Description of the method | Splitting captures | Reducing and clustering the data | Generating artificial doublets | Examining the k-nearest neighbors (kNN) of each cell | Training a classifier | Thresholding | Doublet origins and enrichments | Some important parameters | Expected proportion of doublets | Number of artificial doublets | Frequently-asked questions | I'm getting way too many doublets called - what's going on? | Should I use the cluster-based doublet generation or not? | The clusters don't make any sense! | 'Size factors should be positive' error | Identifying homotypic doublets | What is a sample exactly? Usage with barcoded and 10X Flex data. | How can I make this reproducible? | Can I use this in combination with Seurat or other tools? | How can I call scDblFinder from the command line? | Can this be used with scATACseq data? | Should I run QC cell filtering before or after doublet detection? | What about ambiant RNA decontamination? | Can I combine this method with others? | Session information

Introduction | Applying the scDblFinder method | Using the Amulet method | Combining mehtods | The Clamulet method | Simple p-value combination | References | Session information

tl;dr | Mathematical background | Obtaining explicit calls | Discussion | Session information