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.

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 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

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.

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.

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

This package provides a functional correctness checking suite included in the CUDA toolkit. This suite contains multiple tools that can perform different type of checks. The memcheck tool is capable of precisely detecting and attributing out of bounds and misaligned memory access errors in CUDA applications, and can also report hardware exceptions encountered by the GPU. The racecheck tool can report shared memory data access hazards that can cause data races. The initcheck tool can report cases where the GPU performs uninitialized accesses to global memory. The synccheck tool can report cases where the application is attempting invalid usages of synchronization primitives.

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 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 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 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.

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 Python low-level bindings for NVIDIA CUDA toolkit.

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 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 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 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.