This package contains classes used in model-view-controller (MVC) design.

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

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

This package provides tools for differential expression analysis at both gene and isoform level using RNA-seq data

This package provides tools for analysis of ChIP-seq and other functional sequencing data.

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.

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

The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.

This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.

This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

This package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

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

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 package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

This package contains tools to support the construction of tcltk widgets in R.

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

This package contains data for the ChIPexoQual package, consisting of 3 chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.

This package provides a framework for allele-specific expression investigation using RNA-seq data.

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. It allows searching of biological metadata using various criteria.

This package provides an interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

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