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\_HG-U133B\_probe\_tab.

This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering".

Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman.

Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) assembled using data from public repositories.

Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data (chip h10kcod) assembled using data from public repositories.

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

Package with metadata for genotyping Illumina Omni5 Quad arrays using the crlmm package.

Data used by the barcode package for microarrays of type hgu133a.

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) assembled using data from public repositories.

hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) 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 HG-U95C\_probe\_tab.

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 Hu35KsubC\_probe\_tab.

This package provides a package containing an environment representing the HG-U133A_2.cdf file.

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

Package with metadata for genotyping Illumina 550k arrays using the crlmm package.

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\_MG-430A\_probe\_tab.

Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) 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 HIV PRTPlus 2.CDF file.

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.

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 HG-U133A_tag.CDF file.