This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic search for GWAS. BMC Bioinformatics), BGWAS (Williams, J., Xu, S., Ferreira, M. A.. (2023) "BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies." BMC Bioinformatics), and GINA. All methods currently are for the analysis of Gaussian phenotypes The research related to this package was supported in part by National Science Foundation awards DMS 1853549, DMS 1853556, and DMS 2054173.

Offers a set of autoplot methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using ggtree'. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.

The gene set collection used for the GIGSEA package.

Recurrent breakpoint gene detection on copy number aberration profiles.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95A\_probe\_tab.

Package containing example and annotation data for Hipathia package. Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. Hipathia depends on this package to be functional.

Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) assembled using data from public repositories.

Package with metadata fast genotyping Illumina 1M arrays using the crlmm package.

This package provides a package containing an environment representing the HuGene-1_0-st-v1.cdf file.

This package provides a package containing metadata for Hs6UG171 arrays assembled using data from public repositories.

Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.

Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb) assembled using data from public repositories.

Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) assembled using data from public repositories.

Affymetrix hugene20 annotation data (chip hugene20stprobeset) assembled using data from public repositories.

Package with metadata for genotyping Illumina Omni2.5 Quad arrays using the crlmm package.

Package with metadata for genotyping Illumina 550k arrays using the crlmm package.

Unknown annotation data (chip hguDKFZ31) assembled using data from public repositories.

Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd) assembled using data from public repositories.

Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) assembled using data from public repositories.

This package provides a package containing an environment representing the Hu35KsubB.CDF file.

Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) assembled using data from public repositories.

data from a yeast ChIP-chip experiment.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430\_PM\_probe\_tab.

Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) assembled using data from public repositories.