RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization.

Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod) assembled using data from public repositories.

This package creates a muti-graph web page which allows the interactive exploration of differential analysis tests. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.

This package provides a package containing an environment representing the RAE230A.CDF file.

RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) assembled using data from public repositories.

This package provides a package containing an environment representing the RT_U34.cdf file.

Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.

Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RatToxFX\_probe\_tab.

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

This package provides a collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.

This package provides a collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.

The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.

Base annotation databases for rhesus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) assembled using data from public repositories.

This package provides a programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.

Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) assembled using data from public repositories.

Affymetrix rta10 annotation data (chip rta10probeset) assembled using data from public repositories.

This package provides a web interface to compute transcriptional regulatory modules with rTRM.

raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.

Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.