Pedixplorer
This is the released version of Pedixplorer; for the devel version, see Pedixplorer.
Pedigree Functions
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | Pedixplorer_1.7.1.zip |
| macOS Binary (big-sur-x86_64) | Pedixplorer_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | Pedixplorer_1.8.0.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 |