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methylKit

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing.

Metrics Reloaded

The mission of Metrics Reloaded toolkit is to guide researchers in the selection of appropriate performance metrics for biomedical image analysis problems and to provide a comprehensive online resource for metric-related information and pitfalls.

Algorithm Validation
Problem-Aware Metric Selection
Problem Fingerprint

mHM

The mesoscale Hydrologic Model (mHM) is a well established hydrological model used by the scientific community. It is under active development with dozens of contributors and has an open community always interested in discussions.

Earth & Environment
mesoscale hydrologic model
mHM
+ 2

AGS Script
Fortran Free Form
Python
+ 2

Millepede II

Millepede II has been developed to solve the linear least squares problem with a simultaneous fit of all global and local parameters, irrespectively of the number of local parameters.

Alignment
Large linear equation system
Matter
+ 1

Fortran Free Form
C
Python
+ 2

MO|DE.behave

MO|DE.behave is a Python-based software package for the estimation and simulation of discrete choice models and shall enable rapid quantitative analyses based on survey data on choice behavior, utilizing advanced discrete choice methods. Please refer to 'doi.org/10.21105/joss.05265'.

Python
TeX

MooViE

MooViE is an easy-to-use tool to display multidimensional data with input-output semantics from all research domains. It supports researcher in studying the mapping of several inputs to several outputs in large multivariate data sets.

C++
Data Visualization

C++
CMake
Dockerfile
+ 2

MTRESS

MTRESS (Model Template for Renewable Energy Supply Systems) facilitates the creation of energy system optimisation models for individual residential and commercial buildings as well as for neighbourhoods and entire industrial properties.

Energy
ESD
ESD - Topic 2

Python

NESTML

NESTML is a domain-specific language for neuron and synapse models. It combines an easy to understand, yet powerful syntax with good simulation performance by means of code generation.

Modelling
Simulation
spiking neural networks

Python
Jinja
ANTLR
+ 4

nnU-Net

Automatic configuration and training of U-Net-based segmentation pipelines. Works out-of-the-box for a broad range of datasets from all imaging domain! Supports 2D and 3D (multi-channel) images.

2D images
3D images
semantic segmentation
+ 1

Python
Shell

novoSpaRc

novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data. An existing reference database of marker genes is not required, but significantly enhances performance if available.

Data analysis
open source
single-cell RNA-seq

Jupyter Notebook
HTML
Python

Nexus - Nuclear Elastic X-ray scattering Universal Software

The Nuclear Elastic X-ray scattering Universal Software (Nexus) is a Python package for simulating and fitting of Mossbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities, and polarization dependent electronic scattering.

Mossbauer
Mossbauer spectroscopy
Nuclear resonant scattering
+ 1

C++
SWIG
C
+ 2

ODM2SMS

A tool to migrate sensor metadata from the observation data model to the Helmholtz Sensor Management System via API.

Earth & Environment
metadata
Research Data Management
+ 1

Python