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.

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 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.

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 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.

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 run-time support libraries for NVIDIA GPUs, all of which are proprietary.

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

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

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 minimal low-level profiling API for CUDA.

The NVIDIA Management Library Headers (NVML) is a C-based API for monitoring and managing various states of the NVIDIA GPU devices. It provides a direct access to the queries and commands exposed via nvidia-smi.

This package provides an interface for generating PTX code from both binary and text NVVM IR inputs.

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 an interactive profiler for CUDA and NVIDIA OptiX that provides detailed performance metrics and API debugging via a user interface and command-line tool. Users can run guided analysis and compare results with a customizable and data-driven user interface, as well as post-process and analyze results in their own workflows.

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

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.