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.

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.

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.

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.

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 Python low-level bindings for NVIDIA CUDA toolkit.

This package provides the CUDA compiler and the CUDA run-time support libraries for NVIDIA GPUs, all of which are proprietary.

This package provides the NVIDIA cuBLAS library. It includes several API extensions for providing drop-in industry standard BLAS APIs and GEMM APIs with support for fusions that are highly optimized for NVIDIA GPUs. The cuBLAS library also contains extensions for batched operations, execution across multiple GPUs, and mixed- and low-precision execution with additional tuning for the best performance.

This package provides a set of GPU-accelerated basic linear algebra subroutines used for handling sparse matrices that perform significantly faster than CPU-only alternatives. Depending on the specific operation, the library targets matrices with sparsity ratios in the range between 70%-99.9%.

This package provides the CUDA compiler and the CUDA run-time support libraries for NVIDIA GPUs, all of which are proprietary.

This package provides a binary that prunes host object files and libraries to only contain device code for the specified targets.

This package provides a GPU-accelerated library of primitives for deep neural networks, with highly tuned implementations for standard routines such as forward and backward convolution, attention, matmul, pooling, and normalization.

CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN.

CUTLASS decomposes these ``moving parts'' into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications.

This package provides a high-level library based on the cuBLAS and cuSPARSE libraries. It consists of two modules corresponding to two sets of API: the cuSolver API on a single GPU; and the cuSolverMG API on a single node multiGPU. Each of these can be used independently or in concert with other toolkit libraries. The intent of cuSolver is to provide useful LAPACK-like features, such as common matrix factorization and triangular solve routines for dense matrices, a sparse least-squares solver and an eigenvalue solver. In addition, cuSolver provides a new refactorization library useful for solving sequences of matrices with a shared sparsity pattern.

This package provides a high-performance, GPU accelerated JPEG decoding functionality for image formats commonly used in deep learning and hyperscale multimedia applications. The library offers single and batched JPEG decoding capabilities which efficiently utilize the available GPU resources for optimum performance; and the flexibility for users to manage the memory allocation needed for decoding.

The nvJPEG library enables the following functions: use the JPEG image data stream as input; retrieve the width and height of the image from the data stream, and use this retrieved information to manage the GPU memory allocation and the decoding. A dedicated API is provided for retrieving the image information from the raw JPEG image data stream.

The encoding functions of the nvJPEG library perform GPU-accelerated compression of user’s image data to the JPEG bitstream. User can provide input data in a number of formats and colorspaces, and control the encoding process with parameters. Encoding functionality will allocate temporary buffers using user-provided memory allocator.