Detects haplotype blocks that simultaneously use information about linkage-disequilibrium (LD) decay between blocks and the diversity of haplotypes within blocks. By use of phased single-nucleotide polymorphism (SNP) data, DBlocks partitions a chromosome into a series of adjacent, nonoverlapping blocks. The partition is made by choosing among a family of Markov models for block structure in a chromosomal region. Using computer simulations, MDBlocks can reliably locate the boundaries between blocks at regions of rapid LD decay.
An R package that can handle family and population samples and implements a wide range of region-based association methods including burden tests, functional linear models, and kernel machine-based regression. FREGAT can be used in genome/exome-wide region-based association studies of quantitative traits and candidate gene analysis. FREGAT offers many useful options to empower its users and increase the effectiveness and applicability of region-based association analysis.
Provides an approach dedicated to gene-based association testing. KMgene is an R package that extends sequence kernel association test (SKAT)-type methods for complex traits. The application is able to perform multiple association tests including: (i) continuous family, (ii) binary family, (iii) continuous multivariate, (iv) continuous multivariate family, (v) continuous longitudinal, (vi) and survival.
An efficient tool for region/gene association analysis of quantitative traits in samples of related individuals. This software implements a score-based variance component test to assess the association of a given set of single nucleotide polymorphisms with a continuous phenotype. We compared the performance of our software with that of two existing software for family-based sequence kernel association testing, namely, ASKAT and famSKAT, using the Genetic Analysis Workshop 17 family sample. Results demonstrate that FFBSKAT is several times faster than other available programs. In addition, the calculations of the three-compared software were similarly accurate. The FFBSKAT package is fast, user-friendly, and provides an easy-to-use method to perform whole-exome kernel machine-based regression association analysis of quantitative traits in samples of related individuals.
A region-based association test for familial data under functional linear models. famFLM increases the power of regional association analysis of quantitative traits compared with burden-based and kernel-based methods for the majority of the scenarios.
Investigates genetic variants association with quantitative traits in family data. fanSKAT consists of an extension of sequence kernel association test (SKAT). It can be applied to quantitative traits with unknown or known heritability. This tool can be combined with the collapsing of some very rare genetic variants such as singletons. It is useful for common variant analysis, combined common and rare variant analysis or conditional association analyses.
Produces intragenic or intergenic windows, introns, exons, transcription start sites (TSS) and others from an annotation. Pyicoregion generates exploratory region files like arbitrary length or sliding windows in the exons, introns, intragenic spaces and TSS of any genome in existence. This tool is one of the six modules composing the Pyicoteo suite.