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.

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.

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

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.

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.

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.

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.

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.

This package provides benchmarks for implementations of the Message Passing Interface (MPI). It contains MPI performance measurements for point-to-point and global communication, and file, operations for a range of message sizes. The generated benchmark data fully characterize:

• Performance of a cluster system, including node performance, network latency, and throughput;

• Efficiency of the MPI implementation.

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.

The Phoronix Test Suite is a comprehensive testing and benchmarking platform that provides an extensible framework for which new tests can be easily added. It can carry out both qualitative and quantitative benchmarks in a clean, reproducible, and easy-to-use manner, making it easy to compare one particular setup against another one.

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.

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.

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

The polyester package simulates RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionality for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

This package aims to make NMR spectroscopy data analysis as easy as possible. It only requires a small set of functions to perform an entire analysis. Speaq offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in speaq or available elsewhere on CRAN.

This is a package that can be used for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

This package provides an R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualization tools. Besides providing an easy to use set of tools for manipulating the data from BaseSpace, it also facilitates the access to R's rich environment of statistical and data analysis tools.

This package provides a pipeline for the analysis of GRO-seq data.

The package detects extended diffuse and compact blemishes on microarray chips. Harshlight marks the areas in a collection of chips (affybatch objects). A corrected AffyBatch object will result. The package replaces the defected areas with N/As or the median of the values of the same probe. The new version handles the substitute value as a whole matrix to solve the memory problem.