Colocalization
Summary Table
NAME | CITATION |
---|---|
CoPheScan | Manipur, I., Reales, G., Sul, J. H., Shin, M. K., Longerich, S., Cortes, A., & Wallace, C. (2023). CoPheScan: phenome-wide association studies accounting for linkage disequilibrium. bioRxiv, 2023-06. |
Coloc-susie | Wang, G., Sarkar, A., Carbonetto, P., & Stephens, M. (2020). A simple new approach to variable selection in regression, with application to genetic fine-mapping. BioRxiv, 501114. Wallace, C. (2021). A more accurate method for colocalisation analysis allowing for multiple causal variants. PLoS genetics, 17(9), e1009440. |
Coloc | Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014). Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS genetics, 10(5), e1004383. |
HyPrColoc | Foley, C. N., Staley, J. R., Breen, P. G., Sun, B. B., Kirk, P. D., Burgess, S., & Howson, J. M. (2021). A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nature communications, 12(1), 1-18. |
eCAVIAR | Hormozdiari, F., Van De Bunt, M., Segre, A. V., Li, X., Joo, J. W. J., Bilow, M., ... & Eskin, E. (2016). Colocalization of GWAS and eQTL signals detects target genes. The American Journal of Human Genetics, 99(6), 1245-1260. |
CoPheScan
- NAME : CoPheScan
- SHORT NAME : CoPheScan
- FULL NAME : Coloc adapted Phenome-wide Scan
- URL : https://github.com/ichcha-m/cophescan
- CITATION : Manipur, I., Reales, G., Sul, J. H., Shin, M. K., Longerich, S., Cortes, A., & Wallace, C. (2023). CoPheScan: phenome-wide association studies accounting for linkage disequilibrium. bioRxiv, 2023-06.
- YEAR : 2023
Coloc
- NAME : Coloc
- SHORT NAME : coloc
- FULL NAME : coloc
- URL : https://chr1swallace.github.io/coloc/
- CITATION : Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014). Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS genetics, 10(5), e1004383.
- KEYWORDS : Approximate Bayes Factor (ABF)
Coloc-susie
- NAME : Coloc-susie
- SHORT NAME : Coloc-susie
- FULL NAME : Coloc-susie
- URL : https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html
- CITATION : Wang, G., Sarkar, A., Carbonetto, P., & Stephens, M. (2020). A simple new approach to variable selection in regression, with application to genetic fine-mapping. BioRxiv, 501114. Wallace, C. (2021). A more accurate method for colocalisation analysis allowing for multiple causal variants. PLoS genetics, 17(9), e1009440.
- KEYWORDS : Approximate Bayes Factor (ABF), Sum of Single Effects (SuSiE)
- YEAR : 2020
HyPrColoc
- NAME : HyPrColoc
- SHORT NAME : HyPrColoc
- FULL NAME : Hypothesis Prioritisation for multi-trait Colocalization
- URL : https://github.com/cnfoley/hyprcoloc
- CITATION : Foley, C. N., Staley, J. R., Breen, P. G., Sun, B. B., Kirk, P. D., Burgess, S., & Howson, J. M. (2021). A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nature communications, 12(1), 1-18.
- KEYWORDS : multiple traits,
- YEAR : 2021
eCAVIAR
- NAME : eCAVIAR
- SHORT NAME : eCAVIAR
- FULL NAME : eQTL and GWAS Causal Variant Identification in Associated Regions
- URL : https://github.com/fhormoz/caviar
- CITATION : Hormozdiari, F., Van De Bunt, M., Segre, A. V., Li, X., Joo, J. W. J., Bilow, M., ... & Eskin, E. (2016). Colocalization of GWAS and eQTL signals detects target genes. The American Journal of Human Genetics, 99(6), 1245-1260.