This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

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 was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

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 Hu6800\_probe\_tab.

Agilent Human 1B annotation data (chip hgug4111a) 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.

Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652) assembled using data from public repositories.

Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

This package provides a package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.

This package provides a package containing an environment representing the Hu35KsubC.CDF file.

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.

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.

Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) assembled using data from public repositories.

Affymetrix hugene20 annotation data (chip hugene20stprobeset) assembled using data from public repositories.

Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).

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 Hu35KsubD\_probe\_tab.

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

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

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

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

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

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 HC-G110\_probe\_tab.