PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. Numerical algorithms are implemented in single or double precision (real or complex) using LLt, LDLt and LU with static pivoting (for non symmetric matrices having a symmetric pattern). This solver also provides some low-rank compression methods to reduce the memory footprint and/or the time-to-solution.

Chameleon is a dense linear algebra solver relying on sequential task-based algorithms where sub-tasks of the overall algorithms are submitted to a run-time system. Such a system is a layer between the application and the hardware which handles the scheduling and the effective execution of tasks on the processing units. A run-time system such as StarPU is able to manage automatically data transfers between not shared memory area (CPUs-GPUs, distributed nodes).

PyLops is an open-source Python library focused on providing a backend-agnostic, idiomatic, matrix-free library of linear operators and related computations. It is inspired by the iconic MATLAB Spot – A Linear-Operator Toolbox project.

This software’s goal is to propose a parallel algebraic strategy to decompose a sparse linear system Ax=b, enabling its resolution by a domain decomposition solver. Up to now, Paddle is implemented for the MaPHyS linear solver.

qr_mumps is a software package for the solution of sparse, linear systems on multicore computers based on the QR factorization of the input matrix. Therefore, it is suited to solving sparse least-squares problems and to computing the minimum-norm solution of sparse,underdetermined problems. It can obviously be used for solving square problems in which case the stability provided by the use of orthogonal transformations comes at the cost of a higher operation count with respect to solvers based on, e.g., the LU factorization. qr_mumps supports real and complex, single or double precision arithmetic. This is an experimental version of the package for distributed memory.

Ginkgo is a high-performance numerical linear algebra library for many-core systems, with a focus on solution of sparse linear systems.

Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain-specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.

The Blaze library offers:

• high performance through the integration of BLAS libraries and manually tuned HPC math kernels;

• vectorization by SSE, SSE2, SSE3, SSSE3, SSE4, AVX, AVX2, AVX-512, FMA, SVML, SLEEF, and XSIMD;

• parallel execution by OpenMP, HPX, C++11 threads and Boost threads;

• an intuitive and easy to use API of a domain specific language;

• unified arithmetic with dense and sparse vectors and matrices;

• thoroughly tested matrix and vector arithmetic;

• completely portable, high quality C++ source code.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

mpiGraph is a MPI benchmark to generate network bandwidth images.

The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive meshes, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes.

The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive meshes, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes.

GPCNeT is a benchmark suite that includes simulated network congestion, allowing the benchmarking of network performance in closer-to-real-conditions in HPC networks.

HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

This is an R package which interfaces with the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

Build contrasts for models defined with formulaic.

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.