Table 1.
TIMEOR provides new functionalities to uncover temporal regulatory network and associated mechanisms. Exp.: experimental, Auto.: automated, QC: quality control, co.: correlation, PCA: principal component analysis, norm.: normalization, corr.: correction, DE: differential expression, enrich.: enrichment, TF: transcription factor, GRN: gene regulatory network
| TIMEOR | BioJupies | iDEP | Biowardrobe | RSEQREP | VIPER | T-REx | TuxNet | |
|---|---|---|---|---|---|---|---|---|
| Pre-processing | ||||||||
| Adaptive defaults given exp. design | x | x | ||||||
| Auto. data process from raw .fastqs | x | x | x | x | x | x | ||
| QC, sample co., PCA, norm., corr. | x | x | x | x | x | x | x | x |
| Primary Analysis | ||||||||
| Multiple method compare options | x | x | ||||||
| Close time point DE model(s) | x | |||||||
| Unsupervised time-gene clustering | x | x | x | x | x | x | ||
| Secondary Analysis | ||||||||
| GO, network and pathway enrich. | x | x | x | x | x | x | x | |
| De novo motif analysis | x | |||||||
| Multi-omics data integration | x | x | ||||||
| TF enrichment analysis | x | x | x | |||||
| Temporal GRN construction | x | x | ||||||
| Accessibility Features | ||||||||
| Web interface | x | x | x | x | x | x | ||
| Interactive results | x | x | x | |||||
| Project management | x | x | x | x | ||||
| NUMBER FEATURES | 14 | 7 | 7 | 6 | 6 | 5 | 4 | 4 |