This package provides Affymetrix HG_U95A Array annotation data (chip hgu95a) assembled using data from public repositories.

This R package can annotate variants, compute amino acid coding changes and predict coding outcomes.

Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray's contents in other languages and analysis frameworks.

This package provides R functions for common pre-processing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays.

The package AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to:

• analyze germline epimutations in the context of multi-generational mutation accumulation lines;

• analyze somatic epimutations in the context of plant development and aging.

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

This package provides ChIP-seq data for demonstration purposes in the chromstaR package.

This package offers functionality for taking methtuple or Bismark outputs to calculate ASM scores and compute DAMEs regions. It also offers nice visualization of methyl-circle plots.

This package contains data from untargeted mass spectrometry (MS) of modifications to oxidized cysteine (Cys) 34 in human serum albumin (HSA).

This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.

This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. Its design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on external tools or libraries.

This package provides the HTSlib C library for high-throughput nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

This package provides a data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application.

This package provides a package to perform differential network analysis, differential node analysis (differential coexpression analysis), network and metabolic pathways view.

This package provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.

This package provides raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type.

This package provides data needed to use the ITALICS package.

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types. The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally, we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.