Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
Repository Index
47,133 repositories indexed
97–120 of 217 · Most stars
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
Tools for computational pathology
- machine-learning
- digital-pathology
- computational-pathology
- biomedical-image-processing
Simulation for spacecraft attitude control system analysis and design
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
A thin layer of graphic data types
- graphics-library
- vector
- transformations
- matrix
Exascale multiphase flow solver — 2025 Gordon Bell Prize Finalist | 200T grid points on 43K+ GPUs
- gpu
- exascale
- cfd
- fortran
Multi-Omics Factor Analysis
- multi-omics
- factor-analysis
- mofa
PyKEP is a scientific library providing basic tools for research in interplanetary trajectory design.
- interplanetary
- mission-analysis
- astrodynamics
- aerospace
Iterative Linear Quadratic Regulator with auto-differentiatiable dynamics models
- trajectory-optimization
- differential-dynamic-programming
- theano
- dynamics-models
Multibody dynamics tool kit.
- python
- dynamics
- physics
- simulation
Universal cheminformatics toolkit, utilities and database search tools
- indigo
- bingo
- cheminformatics
- chemistry
Reference mapping for single-cell genomics
- single-cell
- deep-learning
- rna-seq-analysis
- data-integration
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
An extension for Inkscape that makes it easier to draw optical diagrams.
- inkscape-extension
- optics-simulation
- python
- optics
Deep Reinforcement Learning for de-novo Drug Design
- deeplearning
- reinforcement-learning
- cheminformatics
- molecular-modeling
Math.NET Symbolics
- computer-algebra
- mathnet
- dotnet
- fsharp
pyMOR - Model Order Reduction with Python
- python
- model-reduction
- model-order-reduction
- control-systems
Image restoration for fluorescence microscopy
One open-source modeler for structures, heat and fluids, built from scratch in pure Rust: parametric part in, verified results out. Automatic all-hex and tet meshing, our own nonlinear implicit and explicit FEA, heat transfer and lattice Boltzmann CFD — every result checked against theory. For engineers and AI agents alike. Free, forever.
- cae
- cfd
- computational-mechanics
- explicit-dynamics
The TiGL Geometry Library to process aircraft geometries in pre-design.
- opencascade
- aircraft
- c-plus-plus
- geometry
Ark -- Archetype-based Entity Component System (ECS) for Go.
- ecs
- entity-component-system
- go
- golang
OpenAeroStruct is a lightweight tool that performs aerostructural optimization using OpenMDAO.
- openmdao
- optimization
- aerodynamics
- open-source
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
- bioinformatics
- exact-optimization
- metabolomics
- paired-data