Vendors the igraph C source code and builds it into a static library. Other Bioconductor packages can link to libigraph.a in their own C/C++ code. This is intended for packages wrapping C/C++ libraries that depend on the igraph C library and cannot be easily adapted to use the igraph R package.

Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) 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 Rice\_probe\_tab.

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 RT-U34\_probe\_tab.

Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories.

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

Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.

Microarray gene expression data from the study of Vawter et al., 2004.

Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser.

tools for building book.

This package selects genes associated with survival.

This package provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.

Suite of tools for functional analysis.

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

Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) assembled using data from public repositories.

RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.

The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

This package provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

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.

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

This package provides a Redis-based back-end for BiocParallel, enabling an alternative mechanism for distributed computation. The The manager distributes tasks to a worker pool through a central Redis server, rather than directly to workers as with other BiocParallel implementations. This means that the worker pool can change dynamically during job evaluation. All features of BiocParallel are supported, including reproducible random number streams, logging to the manager, and alternative load balancing task distributions.

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).

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