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.

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

HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.

Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb) assembled using data from public repositories.

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

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 contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

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

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

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 Hu35KsubC\_probe\_tab.

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

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis 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-U95B\_probe\_tab.

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.

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

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

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

This package provides a package containing an environment representing the Hu6800subC.CDF file.

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 HG_U95D.CDF file.

HuBMAP provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `bulk_data_transfer()`.

Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.

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.