Repository Index

2D/3D geometry toolkit for Clojure/Clojurescript

• geometry
• visualization
• mesh-generation
• opengl

linalg.h is a single header, public domain, short vector math library for C++

Polygonal Surface Reconstruction from Point Clouds (C++ & Python)

• surface-reconstruction
• urban-modeling
• urban-reconstruction
• primitive-extraction

An axiom-free formalization of category theory in Coq for personal study and practical work

• category-theory
• coq
• monad
• profunctor

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

An open library for the analysis of molecular dynamics trajectories

• molecular-dynamics
• python
• mdtraj
• rmsd

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

A pure Go 3D math library.

2D/3D simplicial mesh generator interface for Python (Triangle, TetGen, gmsh)

• python
• mesh-generation
• scientific-computing
• triangle

R package for detecting doublets in single-cell RNA sequencing data

A Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.

• optimization
• optimization-algorithms
• optimization-methods
• optimization-problem

Dicoogle - Open Source PACS

• dicoogle
• dicom
• pacs
• medical-imaging

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

A C++14-compatible physical units library with no dependencies and a single-file delivery option. Emphasis on safety, accessibility, performance, and developer experience.

• cpp
• cpp14
• cpp14-library
• dimensional-analysis

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

UCE is a zero-shot foundation model for single-cell gene expression data

The TiGL Geometry Library to process aircraft geometries in pre-design.

• opencascade
• aircraft
• c-plus-plus
• geometry

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

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis