Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) assembled using data from public repositories.

Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a) assembled using data from public repositories.

This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.

Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) assembled using data from public repositories.

Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation.

Agilent "Human Genome, Whole" annotation data (chip hgug4112a) assembled using data from public repositories.

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.

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

This package provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute.

Example HapMap data from Illumina 370k BeadChips.

Annotation data file for humanCHRLOC assembled using data from public data repositories.

HVP is a quantitative batch effect metric that estimates the proportion of variance associated with batch effects in a data set.

An R Package for Geneset Enrichment Workflows.

This package provides a package containing an environment representing the HG-U133A_tag.CDF file.

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-U133A\_tag\_probe\_tab.

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\_Rat-Focus\_probe\_tab.

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

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.

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

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

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.

Data used by the barcode package for microarrays of type hgu133plus2.

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.