vkmark offers a suite of scenes that can be used to measure various aspects of Vulkan performance. The way in which each scene is rendered is configurable through a set of options.

A synthetic benchmarking tool to measure peak capabilities of OpenCL devices. It only measures the peak metrics that can be achieved using vector operations and does not represent a real-world use case.

Microbenchmarks suite to evaluate MPI and PGAS (OpenSHMEM, UPC, and UPC++) libraries for CPUs and GPUs.

interbench is designed to benchmark interactivity on Linux. It is designed to measure the effect of changes in Linux kernel design or system configuration changes such as CPU, I/O scheduler and filesystem changes and options. With careful benchmarking, different hardware can be compared.

The anota2seq package provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources, translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source. Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels.

This package provides functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.

This package provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

This package can be used to test two sets of gene lists and visualize the results.

BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with rstan. It provides as output the stanfit object as well as posterior median and credible interval estimates for each correlation element.

This package provides a method for combining single-cell cytometry datasets, which increases the analytical flexibility and the statistical power of the analyses while minimizing technical noise.

This package allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

This is a package with metadata for fast genotyping Affymetrix GenomeWideSnp_6 arrays using the crlmm package.

Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e., differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

This package provides a collection of software tools for calculating distance measures.

This package provides a set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

This package provides methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.

This package provides a collection of compression filters for use with HDF5 datasets.

The AffiXcan package imputes a genetically regulated expression (GReX) for a set of genes in a sample of individuals, using a method based on the total binding affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.

This package is a collection of Strand-seq data. The main purpose is to demonstrate functionalities of the breakpointR package.

Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.

This package provides summarized MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects.