Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.

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.

RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.

RTNsurvival integrates regulons inferred by the RTN package with survival data. For each regulon, a two-tailed GSEA framework computes a differential Enrichment Score (dES) at the individual-sample level. The resulting dES distribution across samples is then used to evaluate survival associations within the cohort. Two primary workflows are supported: (i) Cox proportional hazards models, in which regulon activities are treated as predictors of survival time, and (ii) Kaplan–Meier analyses assessing cohort stratification based on regulon activity. All graphical outputs are customizable according to user specifications.

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 RAE230A\_probe\_tab.

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

Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.

Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster) assembled using data from public repositories.

Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data.

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

Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories.

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.

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.

rifiComparative is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

Affymetrix ragene21 annotation data (chip ragene21stprobeset) 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.

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.

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.

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

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.

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

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

Affymetrix raex10 annotation data (chip raex10stprobeset) assembled using data from public repositories.

Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) assembled using data from public repositories.