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

This package provides more than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.

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.

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.

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.

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

Warpfns is a set of functions within the FSL (FMRIB Software Library) used for handling and applying spatial transformations (warps) to MRI images.

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.

This package is a set of utilities libraries all FSL modules

A wrapper that encapsulates the CEPHES Cmath library.

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.

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

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

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

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

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