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 |