This package implements tools for delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. It also supports partial computation of residuals where selected factors are to be preserved in the output matrix. It implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.

This package provides Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories.

This package is a collection of Strand-seq data. The main purpose is to demonstrate functionalities of the breakpointR package.

This is a package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.

This is an annotation package for Illumina's EPIC methylation arrays.

This package provides a dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessibility for new Bioconductor users is hopefully increased.

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.

This is a package for normalization, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalization procedure is subset-quantile within-array normalization (SWAN), which allows Infinium I and II type probes on a single array to be normalized together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

BgeeCall allows generating present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee.

This package allows biologists to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. This package gives a choice of algorithms for interrogation of genomes with motifs from public sources:

1. a weighted-sum probability matrix;

2. log-probabilities;

3. weighted by relative entropy.

This package can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.

This package provides tools for large-scale identification and advanced visualization of sets of conserved noncoding elements.

R-msigdb provides the Molecular Signatures Database in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object.

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.

This package provides the full genome sequences for Bos taurus (UCSC version bosTau8).

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.

This package provides functions for performing print-run and array level quality assessment.

This package provides classes and statistical methods for large single-nucleotide polymorphism (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

This package provides tools for quality control, analysis and visualization of Illumina DNA methylation array data.

This package exposes an annotation database generated from Ensembl.