This package provides a pipeline for the analysis of GRO-seq data.

This package provides utilities for Receiver Operating Characteristic (ROC) curves, with a focus on micro arrays.

This package provides tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects.

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets.

This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.

tRNAdbImport imports the entries of the tRNAdb and mtRNAdb as GRanges object.

This package provides gene-level read counts from RNA-Seq for gallein-treated and control zebrafish.

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 and classes for de novo prediction of transcription factor binding consensus by heuristic search.

This R package provides tools for handling genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics.

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

The ReportingTools package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser, or in other formats. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.

This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides:

1. low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and

2. a framework that facilitates block processing of array-like objects (typically on-disk objects).

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

This package exposes an annotation database generated from Ensembl.

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.

This package contains functions for exploratory oligonucleotide array analysis.

This package provides a simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. It can also be used for differential expression/2-class data.

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 computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

This package implements some simple capabilities for representing and manipulating hypergraphs.