All software
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
- + 6
Oligo Designer Toolsuite
Oligo Designer Toolsuite is a collection of modules that provides all basic functionalities for custom oligo design pipelines as well as advanced experiment-specific functionalities like machine learning models for oligo specificity prediction within a flexible Python framework.
- bioinformatics
- oligonucleotide design
- Probe Design
- + 1
- Python
- Jupyter Notebook
AutoGaitA
AutoGaitA simplifies, accelerates, and standardises gait analyses after body posture tracking with deep learning algorithms in Python.
- biology
- Gait
- Locomotion
- + 3
- Python
pertpy
Pertpy is a Python-based modular framework for the analysis of large-scale single-cell perturbation experiments.
- perturbation
- scverse
- single-cell RNA-seq
- 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
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
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
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