Table 2.
Comparison of features in the SCTK-QC pipeline with other single-cell analysis toolkits.
| SCTK | PIVOT | Seurat | ascend | scRNABatchQC | Adobo | SCONE | SCHNAPPs | iS-CellR | Ganatum | ASAP browser | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Input format | |||||||||||
| 10x CellRanger | ✓ | ✓ | ✓ | ✓ | |||||||
| SCE Object | ✓ | ✓ | ✓ | ✓ | ✓ | ||||||
| Seurat Object | ✓ | ✓ | |||||||||
| AnnData | ✓ | ✓ | |||||||||
| LOOM | |||||||||||
| BUStools | ✓ | ||||||||||
| SEQC | ✓ | ||||||||||
| STARSolo | ✓ | ||||||||||
| Optimus | ✓ | ||||||||||
| DropEst | ✓ | ||||||||||
| CSV, TXT, and MTX | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
| RSEM | ✓ | ||||||||||
| Ambient droplets detection | ✓ | ||||||||||
| General QC Metrics | |||||||||||
| Total counts | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Number of features detected | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Gene set count (e.g mitochondrial) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||
| Doublet detection | |||||||||||
| scDblFinder | ✓ | ||||||||||
| Scrublet | ✓ | ||||||||||
| doubletFinder | ✓ | ||||||||||
| cxds | ✓ | ||||||||||
| bcds | ✓ | ||||||||||
| cxds/bcds hybrid | ✓ | ||||||||||
| Shiny App/interactive | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
| docker | ✓ | ✓ | ✓ | ✓ | |||||||
| HTML Report | ✓ | ✓ | ✓ | ✓ | |||||||
| Output format | |||||||||||
| RDS | ✓ | ✓ | ✓ | ✓ | |||||||
| AnnData | ✓ | ||||||||||
| hdf5 | ✓ | ✓ | |||||||||
| .txt Flatfile | ✓ | ✓ | |||||||||
| pickle | ✓ | ||||||||||
| joblib | ✓ | ||||||||||
SCTK-QC pipeline supports various types of input, full scRNA-seq quality control pipeline and supports common data structures for data storage.