This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design.

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Roberts2005Annotation Annotation Data (Roberts2005Annotation) assembled using data from public repositories.

RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

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

Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.

Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al.

Agilent Rat annotation data (chip rgug4130a) assembled using data from public repositories.

The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.

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

This package provides a package containing an environment representing the Rat230_2.cdf file.

RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer dual regulons', a new concept that tests whether regulators can co-operate or compete in influencing targets.

The package analyzes the Curve ROC, identificates it among different types of Curve ROC and calculates the area under de curve through the method that is most accuracy. This package is able to standarizate proper and improper pAUC.

Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples.

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

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 Rat230\_2\_probe\_tab.

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

Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) assembled using data from public repositories.

Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

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