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.

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.

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.

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.

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.

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.

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.

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

MCFLIRT (Motion Correction using FMRIB's Linear Image Registration Tool) is a tool within FSL designed to perform motion correction on fMRI data.

Module within FSL that provides advanced functionalities for simulating MRI data, including pulse sequence generation, signal generation, noise addition, and image reconstruction.

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

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

This package is a build dependency of all FSL modules.

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

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

This package is a utility for FSL.

A library that returns the object representing an image/volume once it has been deserialized by the newnifti library. The library implements a data container and common operations for nifti images/volumes

Tool within FSL for FMRIB's Improved Linear Model, used for statistical analysis of fMRI data, enhancing accuracy and reliability.

A library that implement miscellaneous mathematicals methods.