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.

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.

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 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.

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

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

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation.

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.

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 accepts CUDA C++ source code in character string form and creates handles that can be used to obtain the CUDA PTX, for further instrumentation with the CUDA Toolkit. It allows to shrink compilation overhead and simplify application deployment.

This package provides facilities that focus on the simple and efficient generation of high-quality pseudorandom and quasirandom numbers. A pseudorandom sequence of numbers satisfies most of the statistical properties of a truly random sequence but is generated by a deterministic algorithm. A quasirandom sequence of -dimensional points is generated by a deterministic algorithm designed to fill an -dimensional space evenly.

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.

This package decodes (demangles) low-level identifiers that have been mangled by CUDA C++ into user readable names. For every input alphanumeric word, the output of cu++filt is either the demangled name if the name decodes to a CUDA C++ name, or the original name itself.

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.

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 library of functions for performing CUDA accelerated 2D image and signal processing.

The primary library focuses on image processing and is widely applicable for developers in these areas. NPP will evolve over time to encompass more of the compute heavy tasks in a variety of problem domains. The NPP library is written to maximize flexibility, while maintaining high performance.

This binary extracts information from standalone cubin files and presents them in human readable format. The output of nvdisasm includes CUDA assembly code for each kernel, listing of ELF data sections and other CUDA specific sections. Output style and options are controlled through nvdisasm command-line options. nvdisasm also does control flow analysis to annotate jump/branch targets and makes the output easier to read.

This package provides the CUDA C++ developers with building blocks that make it easier to write safe and efficient code. It unifies three essential former CUDA C++ libraries into a single repository:

• Thrust (former repo)

• CUB (former repo)

• libcudacxx (former repo)

This package provides a cross-platform API for annotating source code to provide contextual information to developer tools.

This package provides the CUDA Direct Sparse Solver library.

This package provides cuFFT, the NVIDIA® CUDA® Fast Fourier Transform (FFT) product. It consists of two separate libraries: cuFFT and cuFFTW. The cuFFT library is designed to provide high performance on NVIDIA GPUs. The cuFFTW library is provided as a porting tool to enable users of FFTW to start using NVIDIA GPUs with a minimum amount of effort.

The FFT is a divide-and-conquer algorithm for efficiently computing discrete Fourier transforms of complex or real-valued data sets. It is one of the most important and widely used numerical algorithms in computational physics and general signal processing. The cuFFT library provides a simple interface for computing FFTs on an NVIDIA GPU, which allows users to quickly leverage the floating-point power and parallelism of the GPU in a highly optimized and tested FFT library. The cuFFTW library provides the FFTW3 API to facilitate porting of existing FFTW applications.

This package provides tooling to configure the NVSwitch memory fabrics to form one memory fabric among all participating GPUs, and monitors the NVLinks that support the fabric. See docs for more information.

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.

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.