HTODemux
HTODemux is a tool for Hashing Demultiplexing created by Seurat. More information can be found at:
HTODemux by Seurat: HTODemux .
Parameters - Pre processing
| Parameter | Description | Example |
|---|---|---|
| umi_count | path to filtered rna matrix | –umi_count /”path/rna_filtered/” |
| hto_matrix | path to filtered hto matrix | –umi “/path/hto_filtered/” |
| selection_method | How to choose top variable features | –selection_method “mean.var.plot” |
| ndelim | delimiter from the cell’s column nam | –ndelim “_” |
| number_features | Number of features to be used when finding variable features | –number_features 2000 |
| assay | Choose assay between RNA or HTO | –assay “HTO” |
| margin | Margin for normalisation | –margin 2 |
| norm_method | Normalisation method | –norm_method “CLR” |
Parameters - Demultiplexing
| Parameter | Description | Example |
|---|---|---|
| quantile | quantile for classification | –quantile_hto 0.99 |
| kfunc | clustering function | –kfunc “clara” |
| nstarts | nstarts value for k-means clustering | –nstarts 100 |
| nsamples | Number of samples to be drawn from the dataset used for clustering for kfunc clara | –nsamples 100 |
| init | Initial number of clusters for hashtags | –init NULL |