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 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 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 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.

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 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 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 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 high-level pythonic module 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 Python low-level bindings for NVIDIA CUDA toolkit.

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

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 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 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 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 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.