Pedixplorer
This is the development version of Pedixplorer; for the stable release version, see Pedixplorer.
Pedigree Functions
Bioconductor version: Development (3.22)
Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Author: Louis Le Nezet [aut, cre, ctb]
, Jason Sinnwell [aut], Terry Therneau [aut], Daniel Schaid [ctb], Elizabeth Atkinson [ctb]
Maintainer: Louis Le Nezet <louislenezet at gmail.com>
citation("Pedixplorer")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("Pedixplorer")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Pedixplorer")| Pedigree alignment details | HTML | R Script |
| Pedigree kinship() details | HTML | R Script |
| Pedigree object | HTML | R Script |
| Pedigree plotting details | HTML | R Script |
| Pedixplorer tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Genetics, GraphAndNetwork, Software, Visualization |
| Version | 1.5.6 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl, DT, igraph, shinycssloaders, shinyhelper, shinyjs, shinyjqui, shinyWidgets, htmlwidgets, plotly, colourpicker, shinytoastr |
| System Requirements | |
| URL | https://louislenezet.github.io/Pedixplorer/ |
| Bug Reports | https://github.com/LouisLeNezet/Pedixplorer/issues |
See More
| Suggests | diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools, R.devices, usethis, rlang, magick, cowplot |
| Linking To | |
| Enhances | |
| Depends On Me | pedgene |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Pedixplorer_1.5.6.tar.gz |
| Windows Binary (x86_64) | Pedixplorer_1.5.5.zip (64-bit only) |
| macOS Binary (x86_64) | Pedixplorer_1.5.6.tgz |
| macOS Binary (arm64) | Pedixplorer_1.5.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Pedixplorer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Pedixplorer |
| Bioc Package Browser | https://code.bioconductor.org/browse/Pedixplorer/ |
| Package Short Url | https://bioconductor.org/packages/Pedixplorer/ |
| Package Downloads Report | Download Stats |