Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177.

hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

This package provides a package containing an environment representing the HT_MG-430_PM.cdf file.

Affymetrix hta20 annotation data (chip hta20probeset) assembled using data from public repositories.

HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.

agilent AMADID 026652 annotation data (chip hgug4845a) assembled using data from public repositories.

Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) assembled using data from public repositories.

This package provides a package containing an environment representing the HG_U95A.CDF file.

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

This package provides functions to visualize long vectors of integer data by means of Hilbert curves.

Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800) assembled using data from public repositories.

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 Hu35KsubB\_probe\_tab.

The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw).

HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.

Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) assembled using data from public repositories.

This package provides a package containing an environment representing the HIV PRTPlus 2.CDF file.

This package provides a package containing an environment representing the Hu6800subD.CDF file.

Affymetrix hugene10 annotation data (chip hugene10stprobeset) assembled using data from public repositories.

Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories.

This package provides a package containing an environment representing the Hu35KsubA.CDF file.

This package fits heterogeneous error models for analysis of microarray data.

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.

R objects describing the HEEBO oligo set.