| Contaminant removal |
Is there an option to remove set of contaminants (microbial, ribosomal, etc.) from the read files? |
| Supports other aligners |
Does the tool support alignment files from other tools, instead of performing their own alignment? |
| User-defined gene/region |
Could the user specify a list of regions to perform downstream analysis? |
| Knockdown corrected normalization |
Does the tool enable multiple-sample comparison by facilitating normalization techniques specific to sRNA knockdown studies? |
| Offline |
Can the tool be used offline? |
| Hardcoded genomes |
Is the tool generic? i.e., Is the tool’s ability somehow limited to a set of pre-defined genomes? |
| Quantitative, and Qualitative Plots |
Does the tool support informative plots to gain understanding of the analyzed data (MDS=multi-dimensional scaling, PCA= principal component analysis) |
| Multi-sample comparison plots |
Does the tool provide a comprehensive view of multiple samples (not just differential analysis)? For instance, how does the read distribution vary across multiple samples in different genes of interest? |
| Differential analysis |
Is the tool equipped with modules to perform pairwise differential analysis? |
| Enrichment analysis support |
Is there any support to perform functional enrichment within the tool |
| Interactive interface |
Does the tool have an interactive interface, or plots? |
| miRNA or piRNA specific? |
Is the tool specific to analyze miRNA or piRNA only? |
