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.

This package provides a package containing an environment representing the HG_U95B.CDF file.

This package provides a package containing an environment representing the HT_Rat-Focus.cdf file.

This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.

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

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

Affymetrix Affymetrix Hu35KsubA Array annotation data (chip hu35ksuba) assembled using data from public repositories.

Affymetrix Affymetrix HG_U95B Array annotation data (chip hgu95b) assembled using data from public repositories.

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

An R Package for Geneset Enrichment Workflows.

Affymetrix Affymetrix HG_U95D Array annotation data (chip hgu95d) assembled using data from public repositories.

This package provides a package containing an environment representing the HT_HG-U133_Plus_PM.CDF file.

R objects describing the HEEBO oligo set.

Affymetrix hta20 annotation data (chip hta20transcriptcluster) assembled using data from public repositories.

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

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

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

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

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

Affymetrix hugene20 annotation data (chip hugene20stprobeset) 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\_U95Av2\_probe\_tab.

Affymetrix hta20 annotation data (chip hta20probeset) 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-U95E\_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.