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

Affymetrix huex10 annotation data (chip huex10stprobeset) assembled using data from public repositories.

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

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.

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

This package provides a package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.

This package provides a package containing an environment representing the Hu6800subB.CDF file.

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

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 package containing an environment representing the HC_G110.cdf file.

Unknown annotation data (chip hgubeta7) assembled using data from public repositories.

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 HGU133Plus2_Hs_Hspec.cdf file.

Affymetrix Affymetrix HG_U95D Array annotation data (chip hgu95d) 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 Hu35KsubB\_probe\_tab.

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

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

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

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

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

Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.

This package provides a package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

Example HapMap data from Illumina 370k BeadChips.

This package contains the data used in the vignettes and examples of the h5vc package.