This is a package for inference of protein activity from gene expression data. It includes the VIPER and msVIPER algorithms

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.

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 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 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.

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.

GDRCopy is a low-latency GPU memory copy library based on GPUDirect RDMA technology that allows the CPU to directly map and access GPU memory.

Unified Communication X (UCX) provides an optimized communication layer for message passing (MPI), portable global address space (PGAS) languages and run-time support libraries, as well as RPC and data-centric applications.

UCX utilizes high-speed networks for inter-node communication, and shared memory mechanisms for efficient intra-node communication.

This package adds CUDA support for NVIDIA GPUs.

Collection of miscellaneous C functions and utilities within FSL, providing various helper functions for neuroimaging analysis.

Library within FSL for creating and analyzing shape models of brain structures, aiding in morphometric studies and neuroimaging research.

Module within FSL that facilitates input/output operations using VTK (Visualization Toolkit), enabling advanced visualization and data handling for neuroimaging.

Eddy is a tool within FSL that corrects for eddy current distortions and head movements in diffusion MRI data.

The meshclass module in FSL provides the Mesh class for representing and manipulating 3D models made of triangles, supporting various geometric operations and querie

This package is a utility for FSL.

Verbena is a Bayesian Inference tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.

FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

Tool within FSL for automated segmentation of subcortical brain structures from MRI images, aiding neuroscience research.

This library is likely a component of FSL dedicated to the analysis and visualization of cortical surface data in neuroimaging studies.

FNIRT (FMRIB's Non-linear Image Registration Tool) is a tool for non-linear registration of brain images, used to align images from different subjects or modalities.

Tool within FSL designed for fieldmap-based correction of geometric distortions in EPI images, crucial for accurate fMRI analysis.

Tool within FSL for identifying and analyzing clusters in neuroimaging data, particularly useful for statistical thresholding and inference.