Table 4.
Algorithms and software for integrating GWAS and eQTL data
| Name | Description | LD considered | Programming language | Operatingsystem | Link | Ref. |
|---|---|---|---|---|---|---|
| MetaXcan | Gene expression imputation | Y | Python | Unix/Linux | https://github.com/hakyimlab/MetaXcan | [69] |
| PrediXcan | Gene expression imputation | N | Python | Unix/Linux | https://github.com/hakyimlab/PrediXcan | [70] |
| TWAS / FUSION | Gene expression imputation | Y | R | Unix/Linux, Mac OS, Windows | http://gusevlab.org/projects/fusion/ | [71] |
| COLOC | Co-localization | Y | R | Unix/Linux, Mac OS, Windows | https://github.com/chr1swallace/coloc | [72] |
| MOLOC | Co-localization | Y | R | Unix/Linux, Mac OS, Windows | https://github.com/clagiamba/moloc | [73] |
| ENLOC/fastENLOC | Co-localization | Y | Perl | Unix/Linux, Mac OS, Windows | https://github.com/xqwen/integrative | [73] |
| HyPrColoc | Co-localization | Y | R | Unix/Linux, Mac OS, Windows | https://github.com/jrs95/hyprcoloc | [74] |
| Sherlock | Co-localization | Y | - | Web interface | http://sherlock.ucsf.edu/ | [75] |
| JEPEG | Joint eQTL analysis | Y | C++ | Unix/Linux | https://dleelab.github.io/jepeg/ | [76] |
| CAVIAR | Co-localization | Y | C | Unix/Linux, Mac OS, Windows | http://genetics.cs.ucla.edu/caviar/ | [77] |
| eCAVIAR | Co-localization | Y | C | Unix/Linux, Mac OS, Windows | http://genetics.cs.ucla.edu/caviar/ | [78] |
| GMAC | Mediation analysis | N | R | Unix/Linux, Mac OS, Windows | https://cran.r-project.org/web/packages/GMAC | [79] |
| FINEMAP | Co-localization | Y | C | Unix/Linux, Mac OS | http://www.christianbenner.com/ | [80] |
| eQTLEnrich | Enrichment | Y | MATLAB | Unix/Linux, Mac OS, Windows | https://segrelab.meei.harvard.edu/software/ | [81] |
| S-LDSC | Enrichment | Y | Python | Unix/Linux, Mac OS, Windows | https://github.com/bulik/ldsc | [82] |
| NEO | Structural equation model | N | R | Unix/Linux, Mac OS, Windows | https://labs.genetics.ucla.edu/horvath/htdocs/aten/NEO/ | [83] |
| SMR | Mendelian randomization | Y | C | Unix/Linux, Mac OS, Windows | http://cnsgenomics.com/software/smr | [66] |
| GSMR | Mendelian randomization | Y | R | Unix/Linux, Mac OS, Windows | http://cnsgenomics.com/software/gsmr/ | [84] |
Note: eQTL, expression quantitative trait loci; TWAS, transcriptome-wide association study; JEPEG, joint effect on phenotype of eQTLs/functional SNPs associated with a gene; CAVIAR, causal variants identification in associated regions; eCAVIAR, eQTL and GWAS causal variants identification in associated regions; GMAC, Genomic Mediation Analysis with Adaptive Confounding Adjustment; NEO, Network Edge Orienting; SMR, summary-data-based Mendelian randomization; GSMR, generalized summary-data-based Mendelian randomization.