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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.