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

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

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.

Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation data (chip hwgcod) assembled using data from public repositories.

Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) 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\_HG-U133\_Plus\_PM\_probe\_tab.

This package was created by frmaTools version 1.9.2.

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

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

This package provides functions to visualize long vectors of integer data by means of Hilbert curves.

This package provides a package containing an environment representing the HIV PRTPlus 2.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.

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

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-U95B\_probe\_tab.

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

HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.

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.

Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) 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-U133A\_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 HT\_MG-430B\_probe\_tab.

Package with metadata for genotyping Illumina Omni1 Quad arrays using the crlmm package.

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

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

This package provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and DESeq2` as well as voom differential expression analyses are available.