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.

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

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.

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

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

This package provides a package containing an environment representing the Hu6800.CDF file.

Package with metadata for genotyping Illumina 370kQuad arrays using the crlmm package.

Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) assembled using data from public repositories.

Unknown annotation data (chip hguDKFZ31) assembled using data from public repositories.

Capture Hi-C is a set of techniques that enable the detection of genomic interactions involving regions of interest, known as baits. By focusing on selected loci, these approaches reduce sequencing costs while maintaining high resolution at the level of restriction fragments. HiCaptuRe provides tools to import, annotate, manipulate, and export Capture Hi-C data. The package accounts for the specific structure of bait–otherEnd interactions, facilitates integration with other omics datasets, and enables comparison across samples and conditions.

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

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.

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

This package provides a package containing an environment representing the Hu6800subC.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 HT\_Rat-Focus\_probe\_tab.

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

Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa) assembled using data from public repositories.

Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated).

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

Affymetrix Affymetrix HG_U95C Array annotation data (chip hgu95c) assembled using data from public repositories.

Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod) assembled using data from public repositories.

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

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

HVP is a quantitative batch effect metric that estimates the proportion of variance associated with batch effects in a data set.