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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 (2023) <doi:10.1101/2023.06.29.546856>.

Version: 1.4.1
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: 2024-06-11
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.pdf
Vignettes: CoPheScan: Example with Fixed Priors
CoPheScan: Example with Hierarchical Priors
CoPheScan: Input data
Introduction to CoPheScan

Downloads:

Package source: cophescan_1.4.1.tar.gz
Windows binaries: r-devel: cophescan_1.4.1.zip, r-release: cophescan_1.4.1.zip, r-oldrel: cophescan_1.4.1.zip
macOS binaries: r-release (arm64): cophescan_1.4.1.tgz, r-oldrel (arm64): cophescan_1.4.1.tgz, r-release (x86_64): cophescan_1.4.1.tgz, r-oldrel (x86_64): cophescan_1.4.1.tgz
Old sources: cophescan archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=cophescan to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.