Table 2.
Details on methods applicability. The table lists details concerning each method usability and applicability. Namely, the organisms, cell and tissue types used to develop the tools are specified, as well as details on the code availability.
| Name | Organism | Samples | Code availability |
|---|---|---|---|
| Rodelsperger et al. | Mouse | Embryonic mouse forebrain and limb | – |
| Ernst et al. | Human | 9 cell lines | – |
| Thurman et al. | Human | 125 cell lines | – |
| Shen et al. | Mouse | 19 cell and tissue types | – |
| PreSTIGE | Human | 12 cell lines | Galaxy module |
| IM-PET | Drosophila and human | Drosophila and 12 human cell lines | Galaxy module and archive with a collection of scripts for PERL, Python, Java, R and others tools |
| Andersson et al. | Human | 432 primary cell, 135 tissue and 241 cell lines | – |
| RIPPLE | Human | 4 cell lines | Bitbucket repository with a collection of C++ programs and MATLAB scripts (current version: 1.0) |
| ELMER | Human | 2841 TCGA samples | Bioconductor version: Release (3.9) R package |
| PETModule | Mouse and human | 2 mouse cell lines and 8 human cell lines | Archive with a collection of scripts for Python, Java and other tools |
| TargetFinder | Human | 4 cell lines | GitHub repository with a collection of Python scripts |
| EpiTensor | Human | 5 cell lines | Archive with a collection of scripts for Bash, R, MATLAB and other tools (current version: v0.9) |
| JEME | Human | 935 human primary cell and tissue types | GitHub repository with a collection of scripts for Bash, R and other tools |
| GeneHancer | Human | Cell lines from multiple compendiums | GeneCards web portal |
| McEnhancer | Drosophila | Drosophila embryo development stages | GitHub repository with a collection of scripts for Bash, PERL, R, Python, Java and others tools |
| PEGASUS | Zebrafish and human | Human embryonic stem cells and zebrafish developmental stages | – |
| FOCS | Human | 2630 samples | GitHub repository with a collection of scripts for R |