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193-204 of 233

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
Python
+ 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

openFuelCell2

openFuelCell2 is a computational fluid dynamics (CFD) toolbox for simulating electrochemical devices such as fuel cells and electrolysis. The solver is based on the open-source library, OpenFOAM®.

Electrolyzer
Energy
Fuel cells
+ 1

C
C++
Python
+ 2

openPMD-api

openPMD is an open meta-data schema that provides meaning and self-description for datasets in science and engineering. This library provides a reference API for openPMD data handling, supporting established I/O backends such as HDF5, ADIOS2, JSON and TOML from serial to MPI-parallel workflows.

ADIOS
data
file-format
+ 8

C++
Python
CMake
+ 4

OSADCP Toolbox

Open-source Python toolbox called OSADCP for scientists to convert, clean, calibrate and organize binary raw vessel-mounted Acoustic Doppler Current Profiler (ADCP) data for scientific use. The toolbox is designed to process ADCP measurements in deep water by Teledyne RDI Ocean Surveyor ADCPs.

Data Visualization
Earth & Environment
FAIR Data
+ 5

Python

otter

The otter Framework combines community network analysis using Co-Occurrence networks, Louvain Clustering and Convergent Cross Mapping networks. Funding through the Helmholtz DataHub Initiative; project iLOVE.

Community Dynamics
Earth & Environment
python

Python

PeakPerformance

PeakPerformance is a Python toolbox for estimating peak areas from mass-spectrometry or HPLC datasets under uncertainty. It applies Bayesian inference using the PyMC library to parametric models of peak curves.

Data analysis
Earth & Environment
mass spectrometry
+ 4

Python
TeX

PiGx

PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

HTML
Python
R
+ 7

Potsdam Open-source Radio interferometry Tool (PORT)

PORT is a software package dedicated to the analysis of modern and historical Very Long Baseline Interferometry (VLBI) observations. It is utilized to perform the GFZ VLBI Analysis Center responsibilities, as well as state-of-the-art research in space geodesy, geophysics, and astrometry.

Astrometry
Earth orientation parameters
Reference frames
+ 1

Python
MATLAB
Fortran
+ 2

ProFASi

PROFASI (PROtein Folding and Aggregation SImulator) is a C++ package for HPC Monte Carlo simulations of protein folding and aggregation. It provides an all atom, implicit solvent force field, and a set of tools to perform Monte Carlo simulations.

Monte Carlo
Peptide Aggregation
Protein folding
+ 2

C++
Hack
CMake
+ 2

PyQuickMaps

A slim python library to link maps and sampling data with prediction methods. Needs scipy, numpy, matplotlib, pykrige, osgeo, rasterio.

Data Visualization
Earth & Environment
Predictive Mapping
+ 1

Python