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.

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

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.

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.

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

Topup is a tool within FSL that corrects for susceptibility-induced distortions in echo planar imaging (EPI) data.

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.

Giftiio is a library within FSL for reading and writing GIFTI files, a format used for surface-based data representation in neuroimaging.

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

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

FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.

This meta-package provides all the FSL modules.

Tool within FSL for FMRIB's Local Analysis of Mixed Effects, used for higher-level analysis of fMRI data, providing robust statistical modeling.

It is a set of useful command-line utilities which allow the conversion, processing etc.of Analyze/AVW and Nifti format data sets

cudabasisfield is a FSL module providing helper functions for CUDA operations, facilitating GPU acceleration in FSL tools.

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

FAST4 is an automated segmentation tool in FSL that segments brain images into different tissue types and corrects for bias field inhomogeneities.

A newmat-like wrapper around the Armadillo linear algebra library.

Basisfield is a tool within the FSL (FMRIB Software Library) used to model and correct B0 field inhomogeneities in MRI images, which can cause geometric distortions. It is essential for improving image quality and precision in both clinical and research applications.