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.

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 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.

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.

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

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

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

Module within FSL that provides advanced functionalities for FEAT (FMRI Expert Analysis Tool), including pre-processing steps, model setup, and statistical analysis for fMRI data.

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

This package is a build dependency of all FSL modules.

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

Module within FSL that provides advanced functionalities for noise reduction in MRI data using nonlinear filtering techniques.

Module within FSL that provides visualization functionalities, with its source code available on GitLab.

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

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

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

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.