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

This package was created by frmaTools version 1.9.2.

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.

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

Base annotation databases for human, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) assembled using data from public repositories.

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.

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 provides a package containing an environment representing the HG_U95B.CDF file.

This package provides a package containing an environment representing the HT_HG-U133_Plus_PM.CDF file.

This package provides a healthy dataset with 20 flow cytometry samples used by the flowMatch package.

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

This package was created by frmaTools version 1.13.0.

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

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

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/).

Affymetrix Affymetrix HG_U95B Array annotation data (chip hgu95b) 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.

Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) assembled using data from public repositories.

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

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

This package provides a package containing an environment representing the Hu35KsubD.CDF file.

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