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

The time utility is a simple and often effective way of measuring how long a command takes to run (wall time). Unfortunately, running a command once can give misleading timings. multitime is, in essence, a simple extension to time which runs a command multiple times and prints the timing means, standard deviations, mins, medians, and maxes having done so. This can give a much better understanding of the command's performance.

Locust is a performance testing tool that aims to be easy to use, scriptable and scalable. The test scenarios are described in plain Python. It provides a web-based user interface to visualize the results in real-time, but can also be run non-interactively. Locust is primarily geared toward testing HTTP-based applications or services, but it can be customized to test any system or protocol.

Note: Locust will complain if the available open file descriptors limit for the user is too low. To raise such limit on a Guix System, refer to info guix --index-search=pam-limits-service-type.

sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server. sysbench comes with the following bundled benchmarks:

oltp_*.lua

A collection of OLTP-like database benchmarks.

fileio

A filesystem-level benchmark.

cpu

A simple CPU benchmark.

memory

A memory access benchmark.

threads

A thread-based scheduler benchmark.

mutex

A POSIX mutex benchmark.

It includes features such as:

• Extensive statistics about rate and latency is available, including latency percentiles and histograms.

• Low overhead even with thousands of concurrent threads. sysbench is capable of generating and tracking hundreds of millions of events per second.

• New benchmarks can be easily created by implementing pre-defined hooks in user-provided Lua scripts.

KDiskMark is an HDD and SSD benchmark tool. KDiskMark abstracts away the complexity of the Flexible I/O Tester (fio) command via a convenient graphical user interface (GUI) and handles its output to provide an easy to view and interpret benchmark result. The application is written in C++ with Qt and doesn't have any runtime KDE dependencies. Among its features are:

• Configurable block size, queues, and threads count for each test

• Many languages support

• Report generation.

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.

Benchmark is a library to benchmark code snippets, similar to unit tests.

BenchExec is a framework for reliable benchmarking, which takes care of important low-level details for accurate, precise, and reproducible measurements. In particular, it makes use of cgroups, kernel namespaces, and overlay filesystems to restrict interference of the executed tool with the benchmarking host.

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 BabelStream benchmark measures memory transfer rates between main memory and GPUs. This benchmark is similar in spirit, and based on, John D. McCalpin's STREAM benchmark for CPUs. The version of BabelStream is built targeting AMD GPUs using HIP.

Bonnie++ is a benchmark suite that is aimed at performing a number of simple tests of hard drive and file system performance. Bonnie++ allows you to benchmark how your file systems perform with respect to data read and write speed, the number of seeks that can be performed per second, and the number of file metadata operations that can be performed per second.

fio is a tool that will spawn a number of threads or processes doing a particular type of I/O action as specified by the user. The typical use of fio is to write a job file matching the I/O load one wants to simulate.

Basic4Cseq is an R package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.

Principal Component Analysis (PCA) extracts the fundamental structure of the data without the need to build any model to represent it. This "summary" of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular; users can also identify an optimal number of principal components via different metrics, such as the elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.

MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for:

• covariate-controlled batch- and cohort effect adjustment;

• meta-analysis differential abundance testing;

• meta-analysis unsupervised discrete structure (clustering) discovery;

• meta-analysis unsupervised continuous structure discovery.

This package provides tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.

This package facilitates phyloseq exploration and analysis of taxonomic profiling data. This package provides tools for the manipulation, statistical analysis, and visualization of taxonomic profiling data. In addition to targeted case-control studies, microbiome facilitates scalable exploration of population cohorts. This package supports the independent phyloseq data format and expands the available toolkit in order to facilitate the standardization of the analyses and the development of best practices.

This package provides manifests and annotation for Illumina's 450k array data.

This package offers simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. It works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced negative control samples.

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

This package provides a set of annotation maps for the REACTOME database, assembled using data from REACTOME.

The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.