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.

Affymetrix Affymetrix HG_U95C Array annotation data (chip hgu95c) assembled using data from public repositories.

Affymetrix Affymetrix HT_Rat230_PM Array annotation data (chip htrat230pm) assembled using data from public repositories.

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

Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) assembled using data from public repositories.

Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) assembled using data from public repositories.

Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) assembled using data from public repositories.

This package provides a package containing an environment representing the HT_HG-U133A.cdf file.

data from a yeast ChIP-chip experiment.

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

This package provides a package containing an environment representing the Hu6800subD.CDF file.

Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.

Affymetrix hugene11 annotation data (chip hugene11stprobeset) assembled using data from public repositories.

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

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 Hu35KsubD\_probe\_tab.

Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) assembled using data from public repositories.

Create side-by-side visualizations of tissue thumbnail image and HoverNet cell segmentation with colored cell type labels. Functionality automatically retrieves the thumbnail image associated with a HoverNet JSON file and overlays the segmentation data. This package is intended for researchers working with histopathological images, facilitating exploratory analysis, and integrates with the imageFeatureTCGA Bioconductor package.

Package containing example and annotation data for Hipathia package. Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. Hipathia depends on this package to be functional.

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-430\_PM\_probe\_tab.

HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.

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.

This package provides a function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) 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-U95B\_probe\_tab.