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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

The package contains functions to infer and visualize cell cycle process using Single-cell RNA-Seq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. The tricycle provides a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, it also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

This is a package for the analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Monocle 3 performs clustering, differential expression and trajectory analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle 3 also performs differential expression analysis, clustering, visualization, and other useful tasks on single-cell expression data. It is designed to work with RNA-Seq data, but could be used with other types as well.

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

The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as Latent Dirichlet Allocation (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.

This package provides a method to purify a cell type or cell population of interest from heterogeneous datasets. scGate package automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. scGate takes as input a gene expression matrix stored in a Seurat object and a GM, consisting of a set of marker genes that define the cell population of interest. It evaluates the strength of signature marker expression in each cell using the rank-based method UCell, and then performs kNN smoothing by calculating the mean UCell score across neighboring cells. kNN-smoothing aims at compensating for the large degree of sparsity in scRNAseq data. Finally, a universal threshold over kNN-smoothed signature scores is applied in binary decision trees generated from the user-provided gating model, to annotate cells as either “pure” or “impure”, with respect to the cell population of interest.

This package offers interactive Shiny displays for Bioconductor objects. In addition, this package empowers users to develop engaging visualizations and interfaces for working with Bioconductor data.

This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.