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Contents

  • Coloc
  • Coloc-susie
  • HyPrColoc
  • eCAVIAR
  • CoPheScan

Coloc

  • SHORT 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.

Coloc-susie

  • SHORT NAME: Coloc-susie
  • FULL NAME:
  • URL:https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html
  • YEAR: 2020
  • 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.
  • CITATION: Wallace, C. (2021). A more accurate method for colocalisation analysis allowing for multiple causal variants. PLoS genetics, 17(9), e1009440.

HyPrColoc

  • SHORT NAME: HyPrColoc
  • FULL NAME: Hypothesis Prioritisation for multi-trait Colocalization
  • YEAR: 2021
  • 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.

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.

CoPheScan

  • SHORT NAME: CoPheScan
  • FULL NAME: Coloc adapted Phenome-wide Scan
  • YEAR: 2023
  • 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.