Table 1 Details of all the datasets
From: Evaluating imputation methods for single-cell RNA-seq data
Dataset in the study | Source | Description | Data Size\(^{*}\) | Clusters | Sparsity Rates | Original data type\(^{**}\) | Protocol |
|---|---|---|---|---|---|---|---|
ILC [27] | GSE70580 | Human tonsil Innate lymphoid cells (ILCs) | 26087 \(\times\) 647 | 4 | 87.2% | Raw count | Smart-Seq2 |
HCC [28] | GSE98638 | T cells from hepatocellular carcinoma (HCC) | 14127 \(\times\) 4050 | 11 | 75.0% | Raw count | Smart-Seq2 |
CRC [29] | GSE108989 | T cells from colorectal cancer (CRC) | 12547 \(\times\) 8496 | 20 | 71.6% | Raw count | Smart-Seq2 |
NSCLC [30] | GSE99254 | T cells from non-small cell lung cancer (NSCLC) | 12415 \(\times\) 9051 | 16 | 75.9% | Raw count | Smart-Seq2 |
PBMC\(^{***}\) | – | Peripheral blood mononuclear cells (PBMCs) | 14219 \(\times\) 5356 | 5 | 94.8% | Raw count | Chromium |
BCC [31] | GSE123813 | Single cells from basal cell carcinoma (BCC) | 1000 \(\times\) 50026 | 19 | 55.9% | Raw count | Chromium |
ITC [32] | GSE124731 | Human innate T cells (ITCs) | 13260 \(\times\) 2005 | 7 | 93% | Raw count | Chromium |
DC_human [33] | GSE137710 | Human splenic dendritic cells (DCs) | 14064 \(\times\) 4406 | 7 | 85.6% | Raw count | Chromium |
DC_mouse [33] | GSE137710 | Mouse splenic dendritic cells (DCs) | 12699 \(\times\) 4432 | 7 | 84.6% | Raw count | Chromium |
Melanoma.1 [33] | GSE137710 | Single cells from melanoma | 15292 \(\times\) 8612 | 7 | 92.1% | Raw count | Chromium |
Melanoma.2 [34] | GSE72056 | Single cells from melanoma | 22280 \(\times\) 4636 | 7 | 80.2% | TPM | Smart-Seq2 |
BRCA [35] | GSE75688 | Single cells from breast cancer (BRCA) | 27420 \(\times\) 515 | 5 | 79.0% | TPM | Smart-Seq |
Sim1 | – | – | 600 \(\times\) 2000 | 5 | 30.7% | Raw count | – |
Sim2 | – | – | 600 \(\times\) 2000 | 5 | 50.6% | Raw count | – |
Sim3 | – | – | 600 \(\times\) 2000 | 5 | 70.2% | Raw count | – |
Sim4 | – | – | 600 \(\times\) 2000 | 5 | 89.6% | Raw count | – |