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.

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.

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 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 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 NVIDIA tool for debugging CUDA applications running. CUDA-GDB is an extension to GDB, the GNU Project debugger. The tool provides developers with a mechanism for debugging CUDA applications running on actual hardware. This enables developers to debug applications without the potential variations introduced by simulation and emulation environments.

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

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 set of APIs which can be used at runtime to link together GPU devide code. It supports Link Time Optimization.

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

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 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 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.