Table 2.
Comparison of functionalities offered by miRkit and HTqPCR
| miRkit | HTqPCR | |
|---|---|---|
| Language | R | R |
| Input | Standard output from miScript miRNA PCR Array (Qiagen) technology/ Handles data from multiple plates | Data preprocessing is required/ Only single-plate data, consisting of either 96 or 384 wells |
| Usage | Automatic | Manual (users need to write their one code) |
| Quality control | Yes | Yes |
| Data filtering |
Yes Automatically excluding samples based on NAs and on RTC |
No No standard way implemented |
| Normalization |
Yes Endogenous/exogenous genes |
Yes Scaling up the values or changing the total distribution of values |
| Clustering | Yes | Yes |
| Differential analysis | Yes | Yes |
| Link miRNAs with databases | YES (mirtarbase, tarbase, diana_microt, etc.) | No |
| Enrichment analysis of deregulated genes | Yes (KEGG and GO) | No |