Table 1.
List of machine learning software
| Software name | Machine type | Software type | Application | Data type | Website |
|---|---|---|---|---|---|
| SURF | k-NN | Part of open-source package | Epistatic interactions | SNP | http://www.epistasis.org |
| STIR | k-NN | Standalone Program | Epistatic interactions | SNP | http://insilico.utulsa.edu/software/STIR |
| ReliefSeq | k-NN | Standalone Program | Epistatic interactions | RNA-seq | http://insilico.utulsa.edu/ReliefSeq.php |
| KNN-MDR | k-NN | Standalone program | Epistatic interactions | SNP | n/a |
| GANN | ANN | Standalone program | Gene-based expression association | RNA-seq | n/a |
| ANNI | ANN | Standalone program | Epistatic interactions | SNP | n/a |
| ATHENA | ANN | Standalone program | Epistatic interactions | SNP | https://ritchielab.org/software/athena-downloads |
| Basset | Deep learning | Standalone program | Noncoding annotation | DNA-seq | https://github.com/davek44/Basset |
| DeepSEA | Deep learning | Standalone program | Noncoding annotation | DNA-seq | http://deepsea.princeton.edu/ |
| DeepWAS | Deep learning | Standalone program | GWAS/annotation integration | GWAS | https://github.com/cellmapslab/DeepWAS |
| DFIM | Deep learning | Standalone program | Epistatic interactions | DNA-seq | https://github.com/kundajelab/dfim |
| PrimateAI | Deep learning | Standalone program | Variant pathogenicity | DNA-seq | https://basespace.illumina.com |
| CADD | SVM | Standalone program | Variant pathogenicity | DNA-seq | https://cadd.gs.washington.edu |
| MSIpred | SVM | Python package | Microsatellite instability prediction | WES | https://github.com/bioinfolabmu/MSIpred |
| REVEL | RF | Standalone program | Variant pathogenicity | DNA-seq | https://sites.google.com/site/revelgenomics/ |
| Random jungle | RF | R package | GWAS | SNP | https://r-forge.r-project.org/R/?group_id=741 |
| Ranger | RF | R package | GWAS | SNP | https://cran.r-project.org/web/packages/ranger/index.html |
| Open target genetics | RF | Standalone program | SNP/gene prioritization | GWAS Results | https://genetics.opentargets.org |
| Permuted RF | RF | Standalone program | Epistatic interactions | SNP | n/a |
| RF fishing | RF | Standalone program | Epistatic interactions | SNP | n/a |
| SWSFS | RF | Standalone program | Epistatic interactions | SNP | n/a |
| r2VIM | RF | Standalone program | Epistatic interactions | SNP | https://research.nhgri.nih.gov/software/r2VIM/ |
| Boruta | RF | R package | Epistatic interactions | SNP | https://cran.r-project.org/web/packages/Boruta/index.html |
| Vita | RF | R package | Epistatic interactions | SNP | https://cran.r-project.org/web/packages/vita/index.html |
A list of the software referenced in this review. The columns represent the software names, the type of machine used in the software, the type of software (i.e., whether the software is a stand-alone program or a package), the application for the software, the type of data the software analyzes (note that programs that use SNP data can also use DNA-seq), and the link to download the software (if available)