Q-Q and Manhattan Plots for GWAS Data

Create Q-Q and manhattan plots for GWAS data from PLINK results.

Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Utility Functions for 'spatstat'

Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.

Turner Miscellaneous

Miscellaneous utility functions for data manipulation, data tidying, and working with gene expression data.

Turn Vectors and Lists of Vectors into Indexed Structures

Package designed for working with vectors and lists of vectors, mainly for turning them into other indexed data structures.

Random Generation Functionality for the 'spatstat' Family

Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.

1000 Genomes Project Metadata

Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) and Byrska-Bishop et al. (2022) , and raw data is available at < http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>. See Turner (2022) for more details.

Vector Field Visualizations with 'ggplot2'

A 'ggplot2' extension for visualizing vector fields in two-dimensional space. Provides flexible tools for creating vector and stream field layers, visualizing gradients and potential fields, and smoothing vector and scalar data to estimate underlying patterns.

Extended Generalised Linear Hidden Markov Models

Fits a variety of hidden Markov models, structured in an extended generalized linear model framework. See T. Rolf Turner, Murray A. Cameron, and Peter J. Thomson (1998) , and Rolf Turner (2008) and the references cited therein.

Utilities for SNP-Based Kinship Analysis

Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" .