This package supports the computation of an F-test for the association between expression values and clinical entities. In many cases a two way layout with gene and a dichotomous group as factors will be considered. However, adjustment for other covariates and the analysis of arbitrary clinical variables, interactions, gene co-expression, time series data and so on is also possible. The test is carried out by comparison of corresponding linear models via the extra sum of squares principle.

This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

This package contains example data for Illumina microarray output files, for testing purposes.

This package provides a tool for non linear mapping (non linear regression) using a mixture of regression model and an inverse regression strategy. The methods include the GLLiM model (see Deleforge et al (2015) <DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust version of GLLiM, named SLLiM (see Perthame et al (2016) <DOI:10.1016/j.jmva.2017.09.009>) based on a mixture of Generalized Student distributions. The methods also include BLLiM (see Devijver et al (2017) <arXiv:1701.07899>) which is an extension of GLLiM with a sparse block diagonal structure for large covariance matrices (particularly interesting for transcriptomic data).

This package provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.

This package speeds up the derfinder package when using multiple cores. It is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.

This package provides a consistent interface for downloading, storing, and accessing immune receptor (TCR/BCR) and HLA sequences from IMGT, IPD-IMGT/HLA, and OGRDB (AIRR-C). It supports export to popular analysis tools including MiXCR, TRUST4, Cell Ranger, and IgBLAST. This package serves as a core dependency for immunogenomics packages, ensuring reliable and high-quality sequence access with local caching for reproducibility.

This package implements methods to remove unwanted variation (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

This package provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means.

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

This package provides an interface to the community supported database for amino acid/protein modifications using mass spectrometry.

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Volcano plots represent a useful way to visualise the results of differential expression analyses. This package provides a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding clogging up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via color, shape, size, and shade parameter configurations.

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matrix (PFM), Position Weight Matrix (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

This package provides tools for calculating the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.

This is a package with metadata for genotyping Illumina 370k arrays using the crlmm package.

This package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

This package provides platform design info for Affymetrix Mapping50K_Hind240.

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.