All software
microGWAS
microGWAS is a snakemake-powered pipeline to carry out an end-to-end microbial GWAS analysis. Starting from genome assemblies and a phenotype file, microGWAS will run a number of associations using pyseer, annotate the associations results, and generating a number of functional enrichment tests.
- GWAS
- mGWAS
- Pipeline
- + 2
- Python
- Shell
- 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
DeBCR
DeBCR is a sparsity-efficient deep learning framework for denoising, deblurring, and deconvolving fluorescence microscopy images. Using the m-rBCR model, it restores structural details and improves resolution. It is available as a Python package and napari plugin for efficient image restoration.
- deblurring
- deconvolution
- Deep Learning
- + 3
- Python
- Jupyter Notebook
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
metadeconfoundR
Using non-parametric tests, naive associations between omics features and metadata in cross-sectional data-sets are detected. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests.
- R
pyMarAI
Neural network model and PyQt5-based user interface for image segmentation of microscopic tumor spheroids. Usable with nnU-Net deep-learning framework. Trained on microscopic images of mouse pheochromocytoma (MPC) cells. Provides pipelines for handling data, running delineation, curating results...
- Artifical Intelligence
- cancer
- Convolutional Neural Networks
- + 6
- Python
PyPlaque
PyPlaque is an open-source Python package for automated analysis of virus plaque assays. It quantifies plaque morphology, size, and intensity from plate images, integrates with Python data tools, and enables reproducible, customizable workflows for high-throughput infection biology studies.
- Health
- Image processing
- Omics
- + 1
- Jupyter Notebook
- Python
scPower
scPower is a statistical framework for design and power analysis of multi-sample single cell transcriptomics experiments. It enables users to identify the optimal experimental parameters for cell type specific inter-individual DE and eQTL analysis using single cell RNA-seq data given a fixed budget.
- Experimental design
- Health
- scRNA-seq
- + 1
- R
- HTML
- CSS
SIMPA - The toolkit for Simulation and Image Processing for Photonics and Acoustics
SIMPA facilitates realistic simulations for optical and acoustic imaging modalities by providing a communication layer between various forward and inverse models. Non-experts can easily create sensible simulations from default parameters and domain experts can set up a highly customisable pipeline.
- acoustic imaging
- open-source
- optical imaging
- + 2
- Python
- MATLAB
- Shell
- + 1
VoltRon
VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is also capable of analyzing multiple types of spatially-aware data modalities.
- Genomics
- spatial omics
- R
- C++
- Dockerfile
- + 2
VoxTell
VoxTell is a vision–language model for text-driven 3D medical image segmentation, enabling analysis of anatomical structures and pathologies across CT, MRI, and PET, including open-set and clinically described targets beyond predefined label sets.
- Health
- Image processing
- Machine learning
- + 2
- Python