Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) assembled using data from public repositories.

The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

Automatically generated RnBeads annotation package for the assembly mm10.

This package provides a suite of classes and functions for randomizing patients in clinical trials.

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.

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.

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.

RNA-sense tool compares RNA-seq time curves in two experimental conditions, i.e. wild-type and mutant, and works in three steps. At Step 1, it builds expression profile for each transcript in one condition (i.e. wild-type) and tests if the transcript abundance grows or decays significantly. Dynamic transcripts are then sorted to non-overlapping groups (time profiles) by the time point of switch up or down. At Step 2, RNA-sense outputs the groups of differentially expressed transcripts, which are up- or downregulated in the mutant compared to the wild-type at each time point. At Step 3, Correlations (Fisher's exact test) between the outputs of Step 1 (switch up- and switch down- time profile groups) and the outputs of Step2 (differentially expressed transcript groups) are calculated. The results of the correlation analysis are printed as two-dimensional color plot, with time profiles and differential expression groups at y- and x-axis, respectively, and facilitates the biological interpretation of the data.

RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages.

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

This package provides a package containing an environment representing the RG_U34C.cdf file.

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

RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.

R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Affymetrix Affymetrix RN_U34 Array annotation data (chip rnu34) assembled using data from public repositories.

Automatically generated RnBeads annotation package for the assembly mm9.

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.

RNAmodR.AlkAnilineSeq implements the detection of m7G, m3C and D modifications on RNA from experimental data generated with the AlkAnilineSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search.

This package was created with the help of frmaTools version 1.24.0.