agilent AMADID 026652 annotation data (chip hgug4845a) 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-Focus\_probe\_tab.

Affymetrix Affymetrix HG_U95E Array annotation data (chip hgu95e) 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 HT\_Rat230\_PM\_probe\_tab.

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

Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b) assembled using data from public repositories.

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

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

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

This package provides a package containing an environment representing the HGU133Plus2_Hs_Hspec.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\_HG-U133B\_probe\_tab.

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

Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data. HPAanalyze is designed to fullfill 3 main tasks: (1) Import, subsetting and export downloadable datasets; (2) Visualization of downloadable datasets for exploratory analysis; and (3) Working with the individual XML files. This package aims to serve researchers with little programming experience, but also allow power users to use the imported data as desired.

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

Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) 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-U133B\_probe\_tab.

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.

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.

Dataset package containing gene and isoform count matrices, and sample metadata for long-read direct cDNA sequencing of human retinal organoids, 2D retinal ganglion cell (RGC) cultures, and flowthrough fractions from H9 and EP1 iPSC cell lines. Data were generated using Oxford Nanopore Technology (ONT) direct cDNA sequencing and mapped to the GRCh38 reference genome (GENCODE v46 annotation). The package provides accessor functions returning SummarizedExperiment objects for gene-level counts, isoform-level counts, and a matrix of allele-specific expression (ASE) gene counts. Data files are stored in flat CSV format in an Open Science Framework (OSF) repository and cached locally via BiocFileCache.

Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip hthgu133pluspm) assembled using data from public repositories.

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).

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/).

This package provides a package containing an environment representing the Hu35KsubA.CDF file.

The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.