DemuxEM
DemuxEM is a tool developped by Pegasus. More information can be found at:
DemuxEM by Pegasus: DemuxEM .
| Parameter | Description | Example |
|---|---|---|
| rna_raw | path to raw RNA matrix | –rna_raw “path/rna_raw/” |
| hto_matrix | path to HTO matrix | –hto_raw /”path/hto_raw/” |
| alpha | The Dirichlet prior concentration parameter alpha on samples. | –alpha 0.0 |
| alpha_noise | The Dirichlet prior concenration parameter on the background noise | –alpha_noise 1.0 |
| tol | Threshold used for the EM convergence | –tol 1e-6 |
| n_threads | Number of threads to use, must be a positive number | –n_threads 1 |
| min_signal | Any cell/nucleus with less than min_signal hashtags from the signal will be marked as unknown | –min_signal 10.0 |
The description of this parameters were provided by the library. They can also be found in the link above.