Table 1 Datasets used to benchmark each part of the CytoPheno tool.
From: Automated descriptive cell type naming in flow and mass cytometry with CytoPheno
Part | Benchmark | Type | Species | Platform | Sample type | # Markers used for phenotyping | # Cell types (original) | # Cell types used for testing (Part 3) |
|---|---|---|---|---|---|---|---|---|
1–3 | Samusik | Expression values | Mouse | Mass cytometry | Bone marrow | 28 | 24 | 23 |
Kimmey | Expression values | Human | Mass cytometry | PBMC | 11 | 9 | 7 | |
Spectral | Expression values | Human | Spectral flow cytometry | PBMC | 8 | 8 | 8 | |
2 | Human marker set | Marker names | Human | Flow and mass cytometry | NA | |||
Mouse marker set | Marker names | Mouse | Flow and mass cytometry | NA | ||||
3 | OMIP 54 | Marker definitions | Mouse | Mass cytometry | Brain, spleen, bone marrow | 12 | 9 | 8 |
OMIP 63 | Marker definitions | Human | Flow cytometry | PBMC | 23 | 28 | 23 | |
OMIP 78 | Marker definitions | Human | Flow cytometry | PBMC | 24 | 25 | 23 | |
