Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.

Affymetrix Human Genome 219 Plate annotation data (chip hgu219) assembled using data from public repositories.

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

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

This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).

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

This package provides a package containing an environment representing the HG_U95D.CDF file.

RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen) assembled using data from public repositories.

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.

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

Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b) 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 was automatically created by package AnnotationDbi version 1.11.8. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg19.

Agilent "Human Genome, Whole" annotation data (chip hgug4112a) assembled using data from public repositories.

The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.

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

The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

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

Affymetrix hta20 annotation data (chip hta20probeset) assembled using data from public repositories.

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 HT\_Rat230\_PM\_probe\_tab.

This package provides a package containing an environment representing the HT_Rat230_PM.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.

Example HapMap data from Illumina 370k BeadChips.