All software
QUAST
QUAST is a state-of-the-art tool for (meta)genome assembly evaluation, computing over 50 quality metrics and presenting results in plain text, static plots, and interactive HTML reports.
- Data Visualization
- FAIR Software
- Genome assembly
- + 4
- AMPL
- C++
- Python
- + 12
maftools
maftools is a comprehensive toolkit for processing somatic variants from cohort-based cancer genomic studies
- cancer
- Classification
- Data analysis
- + 14
- R
- C
- CSS
anvi'o
anvi'o is an open-source software platform for microbial 'omics research enabling analysis and visualization of 'omics data. In development since 2014, it is currently being maintained by the Ecosystem Data Science group at the Helmholtz Institute for Functional Marine Biodiversity.
- Data analysis
- Data Visualization
- Metagenomics
- + 4
- Python
- JavaScript
- HTML
- + 5
MIRP
MIRP is a python package for quantitative analysis of medical images. It focuses on processing images for integration with radiomics workflows. These workflows either use quantitative features computed using MIRP, or directly use MIRP to process images as input for deep learning models.
- Medical Image Processing
- python
- radiomics
- Python
- Jupyter Notebook
- R
- + 2
SpatialData framework
SpatialData is an open and interoperable data framework for ingesting, representing, processing and visualizing spatial omics datasets.
- Data Visualization
- FAIR Data
- Multi omics
- + 3
- Python
- Dockerfile
cola
Subgroup classification is a basic task in genomic data analysis. The cola package provides a general framework for subgroup classification by consensus partitioning.
- Data analysis
- Data Visualization
- FAIR Data
- + 3
- R
- C++
MEmilio
MEmilio implements various models for infectious disease dynamics, from compartmental to agent-based models. Through efficient implementation and parallelization, MEmilio brings cutting edge and compute intensive models to a large scale, enabling high-resolution spatiotemporal disease dynamics.
- Agent-based Model
- C++
- compartmental model
- + 12
- C++
- Python
- CMake
- + 2
Aviator
Aviator is a web service facilitating easy surveillance of scientific online tools. It currently checks more than 13,000 websites twice a day for availability and saves numerous features (response time, RAM usage security certificates, analytic tools / trackers, etc.) in a FAIR data repository.
- Data Visualization
- FAIR Data
- FAIR Software
- + 8
- Python
- HTML
- JavaScript
- + 5
AutoGaitA
AutoGaitA simplifies, accelerates, and standardises gait analyses after body posture tracking with deep learning algorithms in Python.
- biology
- Gait
- Locomotion
- + 3
- Python
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
flexynesis
A deep-learning based multi-omics sequencing data integration suite
- Python
- Scheme
- Dockerfile
Lightning UQ Box
The lightning-uq-box is a PyTorch library that provides various Uncertainty Quantification (UQ) techniques for modern neural network architectures.
- Deep Learning
- python
- uncertainty quantification
- Python