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.

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.

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 enables the creation of profiling and tracing tools that target CUDA applications and give insight into the CPU and GPU behavior of CUDA applications. It provides the following APIs:

• the Activity API,

• the Callback API,

• the Event API,

• the Metric API,

• the Profiling API,

• the PC Sampling API,

• the Checkpoint API.

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 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 the CUDA Direct Sparse Solver library.

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

This package provides a set of APIs which can be used at runtime to combine multiple CUDA objects into one CUDA fat binary (fatbin). The APIs accept inputs in multiple formats, either device cubins, PTX, or LTO-IR. The output is a fatbin that can be loaded by cuModuleLoadData of the CUDA Driver API. The functionality in this library is similar to the fatbinary offline tool in the CUDA toolkit, with the following advantages:

• Support for runtime fatbin creation.

• The clients get fine grain control over the input process.

• Supports direct input from memory, rather than requiring inputs be written to files.

This package provides Python low-level bindings for NVIDIA CUDA toolkit.

This package provides a system-wide performance analysis tool designed to visualize an application’s algorithms, identify the largest opportunities to optimize, and tune to scale efficiently across any quantity or size of CPUs and GPUs,from large servers to small systems-on-a-chip.

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

OpenCL (Open Computing Language) is a multi-vendor open standard for general-purpose parallel programming of heterogeneous systems that include CPUs, GPUs and other processors. This package provides the API to use OpenCL on NVIDIA GPUs.

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 provides a high-level pythonic module for NVIDIA CUDA toolkit.

This binary extracts information from CUDA binary files (both standalone and those embedded in host binaries) and presents them in human readable format. The output of cuobjdump includes CUDA assembly code for each kernel, CUDA ELF section headers, string tables, relocators and other CUDA specific sections. It also extracts embedded ptx text from host binaries.

This package provides a C++ header-only library that wraps the NVIDIA CUDA Deep Neural Network library (cuDNN) C backend API. This entry point to the same API is less verbose (without loss of control), and adds functionality on top of the backend API, such as errata filters and autotuning.