CRAN: Package cophescan

cophescan: Adaptation of the Coloc Method for PheWAS

A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see Manipur et al (2024, Nature Communications) <doi:10.1038/s41467-024-49990-8>.

Version: 1.4.2

Depends: R (≥ 3.5.0)

Imports: Rcpp (≥ 1.0.7), coloc, data.table, ggplot2, ggrepel, pheatmap, methods, viridis, stats, grDevices, magrittr, utils, matrixStats, dplyr

LinkingTo: Rcpp, RcppArmadillo

Suggests: knitr, testthat (≥ 3.0.0), rmarkdown, RColorBrewer, ggpubr

Published: 2025年07月30日

DOI: 10.32614/CRAN.package.cophescan

Author: Ichcha Manipur [aut, cre], Chris Wallace [aut]

Maintainer: Ichcha Manipur <im504 at cam.ac.uk>

BugReports: https://github.com/ichcha-m/cophescan/issues

License: GPL-3

URL: https://github.com/ichcha-m/cophescan, https://ichcha-m.github.io/cophescan/

NeedsCompilation: yes

Citation: cophescan citation info

Materials: README, NEWS

CRAN checks: cophescan results

Documentation:

Reference manual: cophescan.html , cophescan.pdf

Vignettes: CoPheScan: Example with Fixed Priors (source, R code)
CoPheScan: Example with Hierarchical Priors (source, R code)
CoPheScan: Input data (source, R code)
Introduction to CoPheScan (source, R code)

Downloads:

Package source: cophescan_1.4.2.tar.gz

Windows binaries: r-devel: cophescan_1.4.2.zip, r-release: cophescan_1.4.2.zip, r-oldrel: cophescan_1.4.2.zip

macOS binaries: r-release (arm64): cophescan_1.4.2.tgz, r-oldrel (arm64): cophescan_1.4.2.tgz, r-release (x86_64): cophescan_1.4.2.tgz, r-oldrel (x86_64): cophescan_1.4.2.tgz

Old sources: cophescan archive

Linking:

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