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).

An interactive tool to visualize long vectors of integer data by means of Hilbert curves.

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

Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

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-U95D\_probe\_tab.

This package provides a package built under the Bayesian framework of applying hierarchical latent Dirichlet allocation. It statistically tests whether the mutational exposures of mutational signatures (Shiraishi-model signatures) are different between two groups. The package also provides inference and visualization.

This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.

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

This package provides a package containing an environment representing the HG-U219.cdf file.

Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) assembled using data from public repositories.

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

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\_U95Av2\_probe\_tab.

Annotation data file for hgu2beta7 assembled using data from public data repositories.

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.

Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip hthgu133pluspm) 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.

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

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

Package with metadata for genotyping Illumina CytoSNP 12 arrays using the crlmm package.

Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories.

The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie.

Base annotation databases for human, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

Package with metadata for genotyping Illumina Omni5 Quad arrays using the crlmm package.

Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) assembled using data from public repositories.