All software

InteractiveComplexHeatmap

InteractiveComplexHeatmap is an R package that converts static heatmaps produced from ComplexHeatmap package into an interactive Shiny app only with one extra line of code.

SeisBench: A toolbox for machine learning in seismology

SeisBench is an open-source Python toolbox for machine learning in seismology. It brings together the whole machine learning model lifecycle: datasets and benchmarks, models and training pipelines, and efficient implementations for deploying the models in production.

simplifyEnrichment

A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.

EnrichedHeatmap

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. The EnrichedHeatmap package provides advanced solutions for normalizing genomic signals within target regions as well as offering highly customizable visualizations.

FastSurfer

FastSurfer is a fast and accurate deep-learning pipeline for the analysis of human brain MRI. FastSurfer provides a fully compatible FreeSurfer alternative for volumetric and surface-based thickness analysis, also supporting sub-mm resolutions, and sub-segmentation of neuroanatomical structures.

CellDetection

An open-source Python package, offering advanced AI methods for the identification and segmentation of biomedical objects, such as cells, in image data. Includes trained models that work out-of-the-box for a wide range of use cases.

FlexiGIS

FlexiGIS is a software tool for processing and analysing GIS-based data to design urban energy systems. Models developed with FlexiGIS enable the exploration and assessment of flexibility options in cities.

rGREAT

GREAT is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm, also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application.

multiGSEA

The multiGSEA R package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers. The enrichment is calculated for each omics layer separately and aggregated p-values are calculated afterwards to derive a composite multi-omics pathway enrichment.

ESMValCore

ETHOS.RESKit

RESKit aids with the broad-scale simulation of renewable energy systems, primarily for the purpose of input generation to Energy System Design Models.

alpaka

The alpaka library is a header-only C++17 abstraction framework designed for computing accelerator development. It enables developers to implement algorithms once and execute them across a range of platforms, including x86, ARM, and RISC-V CPUs, as well as accelerators from NVIDIA, AMD, and Intel.