All software
scanpy
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
- bioinformatics
- Data analysis
- python
- Python
- R
2x2, 3x3 and nxn Space-Filling Curves
Implementation of all possible forms of 2x2 and 3x3 space-filling curves, and nxn curves expanded from any specific level-1 units. It also implements the H-curve and the three-dimensional Hilbert curve.
- Data analysis
- Data Visualization
- open source
- R
- C++
- C
CDS ToolChain
The CDS ToolChain is being developed as part of the INTERPOLAR project of the Medical Informatics Initiative (MII). The CDS ToolChain is typically used in an MII data integration center (DIZ) and processes FHIR resources that comply with the MII Core Data Set (CDS) specification.
- FHIR
- OpenSource
- R
- PLpgSQL
- Shell
- + 2
CIMPredict
CIMPredict delivers an alternative to the FRAX fracture risk calculator for osteoporosis patients based on a new Calcium isotope marker in blood.
- Blue Health Tech
- Data analysis
- Health
- + 2
- Python
- R
dataquieR
dataquieR is an R package designed to conduct automated and standardized data quality assessments. It can be applied to all sorts of tabular data. Spreadsheet-type metadata can be used to specify descriptions, expectations, and requirements about the data.
- Cohort studies
- data quality
- data quality assessment
- + 11
- R
- JavaScript
- HTML
- + 1
DataSHIELD
DataSHIELD ecosystem is an infrastructure and series of R packages that enables the remote and non-disclosive analysis of sensitive research data. It has been used with real world and consented research data for over 10 years.
- data privacy
- OpenSource
- R
- R
Habitat Sampler
Habitat Sampler (HaSa, Community Version), an innovative tool that autonomously generates representative reference samples for predictive modelling of surface class probabilities.
- autonomous sampling
- Earth & Environment
- image classification
- + 1
- HTML
- R
- Shell
InteractiveVis
The InteractiveVis software framework provides a blueprint for evaluating 3D datasets with convolutional neural networks (CNNs), and for deriving and visualizing CNN relevance maps. This tool was developed and tested for disease detection in MRI scans. We plan to extend it to other domains.
- Data Visualization
- MRI
- open source
- + 1
- Jupyter Notebook
- HTML
- MATLAB
- + 5
KaRRi - Karlsruhe Rapid Ridesharing
KaRRi is a state-of-the-art dispatcher for the dynamic taxi sharing problem with meeting points. KaRRi utilizes highly engineered many-to-many shortest path queries to compute optimal assignments of riders to vehicles and according meeting points within milliseconds.
- algorithm engineering
- algorithms
- Future Mobility
- + 11
- C++
- CMake
- Shell
- + 3
MemRBC
MemRBC is an R package for spectral modeling of red blood cell shapes in R. It is the result of open science research, demonstrating the idea of hi-level apps with metadata creation in a lightweight obejct oriented approach.
- cell shape
- Helfrich
- R
- + 5
- R
- C++
- C
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.
- R
- C++
- TeX
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