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

A collection of host-based and device-based microbenchmarks for MPI communication with CUDA support.

This package is used for the detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. It also provides the possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots.

Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.

This is a package for inference of protein activity from gene expression data. It includes the VIPER and msVIPER algorithms

This package provides more than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.

This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.

DoRothEA is a gene regulatory network containing signed transcription factor. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

RAJA offers portable, parallel loop execution by providing building blocks that extend the generally-accepted parallel for idiom. RAJA relies on standard C++14 features.

CAMP collects a variety of macros and metaprogramming facilities for C++ projects. It's in the direction of projects like metal (a major influence) but with a focus on wide compiler compatibility across HPC-oriented systems.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

CHAI is a C++ libary providing an array object that can be used transparently in multiple memory spaces. Data is automatically migrated based on copy-construction, allowing for correct data access regardless of location. CHAI can be used standalone, but is best when paired with the RAJA library, which has built-in CHAI integration that takes care of everything.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources.

The rfacts package is an R interface to the Fixed and Adaptive Clinical Trial Simulator FACTS. It programmatically invokes FACTS to run clinical trial simulations. It aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility.

This package provides several cubic spline interpolation methods of H. Akima for irregular and regular gridded data are available through this package, both for the bivariate case and univariate case. Linear interpolation of irregular gridded data is also covered. A bilinear interpolator for regular grids was also added for comparison with the bicubic interpolator on regular grids.

This package provides a <bits/floatn.h> header to override that of glibc and disable float128 support. This is required allow the use of nvcc with CUDA 8.0 and glibc 2.26+. Otherwise, nvcc fails like this:

/gnu/store/…-glibc-2.26.105-g0890d5379c/include/bits/floatn.h(61): error: invalid argument to attribute "__mode__"

/gnu/store/…-glibc-2.26.105-g0890d5379c/include/bits/floatn.h(73): error: identifier "__float128" is undefined

See also https://devtalk.nvidia.com/default/topic/1023776/cuda-programming-and-performance/-request-add-nvcc-compatibility-with-glibc-2-26/1.

This package provides a set of APIs which can be used at runtime to link together GPU devide code. It supports Link Time Optimization.

This package provides a command-line tool to profile CUDA kernels. It enables the collection of a timeline of CUDA-related activities on both CPU and GPU, including kernel execution, memory transfers, memory set and CUDA API calls and events or metrics for CUDA kernels.