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.

Data used by the barcode package for microarrays of type hgu133a.

This package provides a package containing an environment representing the HG-U133B.cdf file.

Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) assembled using data from public repositories.

Package with metadata for genotyping Illumina Omni1 Quad arrays using the crlmm package.

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.

Dataset package containing gene and isoform count matrices, and sample metadata for long-read direct cDNA sequencing of human retinal organoids, 2D retinal ganglion cell (RGC) cultures, and flowthrough fractions from H9 and EP1 iPSC cell lines. Data were generated using Oxford Nanopore Technology (ONT) direct cDNA sequencing and mapped to the GRCh38 reference genome (GENCODE v46 annotation). The package provides accessor functions returning SummarizedExperiment objects for gene-level counts, isoform-level counts, and a matrix of allele-specific expression (ASE) gene counts. Data files are stored in flat CSV format in an Open Science Framework (OSF) repository and cached locally via BiocFileCache.

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.

Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.

HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.

Package with metadata for genotyping Illumina 610kQuad arrays using the crlmm package.

Sample dataset obtained from http://www.hapmap.org.

Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) 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 HG-Focus\_probe\_tab.

Package with metadata for genotyping Illumina 660kQuad arrays using the crlmm package.

This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.

This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881.".

This package provides a package containing an environment representing the HG_U95E.CDF file.

Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) 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.

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

The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object.

This package provides R bindings for HiSpa, a hierarchical Bayesian model for inferring three-dimensional chromatin structures from Hi-C contact matrices using Markov Chain Monte Carlo (MCMC) sampling. The package implements a cluster-based hierarchical approach that efficiently handles large-scale Hi-C datasets. It uses Rcpp and RcppArmadillo for efficient C++ integration with the original HiSpa C++ implementation, enabling fast computation of chromatin structure inference through parallel MCMC sampling.

Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm) assembled using data from public repositories.