Repository Index

Main yt repository

• data
• visualization
• analysis
• python

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

bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.

• huggingface
• bert
• chemical-modelling
• chemical-smiles-data

Official repository for the ProteinGym benchmarks

• benchmark
• computational-biology
• protein
• protein-design

Sequential regulatory activity predictions with deep convolutional neural networks.

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

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

formally verified category theory library

• category-theory
• formal-verification
• formal-proofs

CoqHammer: An Automated Reasoning Hammer Tool for Rocq - Proof Automation for Dependent Type Theory

• coq
• hammer
• automation
• proof-search

Allocators, I/O streams, math, geometry, image and audio processing for D

• utility-library
• dlang
• linear-algebra
• computational-geometry

Associated Repository for "Translation between Molecules and Natural Language"

The official NFFT library repository

• nfft
• fftw
• fourier-transform
• c

Repository for Nicheformer: a foundation model for single-cell and spatial omics

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

The repository host gives no description.

Inner ear models for Python

• python
• cochlea
• inner-ear
• model

Coq Repository at Nijmegen [maintainers=@spitters,@VincentSe,@Lysxia]

• coq-library
• real-number
• coq
• coq-ci

Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.

• foundation-models
• gpt
• single-cell

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

• minerva
• microscopy
• ome
• immunofluorescence

Graph Theory [maintainers=@chdoc,@damien-pous]

• coq
• graph-theory
• mathcomp
• docker-coq-action

The d-SEAMS C++ core engine

• molecular-dynamics-simulation
• molecular-dynamics
• trajectory-analysis
• lua

Updated infix.cl of the CMU AI repository, originally written by Mark Kantrowitz

• infix-notation
• common-lisp
• mathematics

Qurry (was) a prototype for a functional quantum programming language. It incorporated many aspects of functional programming (Haskell, Clojure), but also took standard design philosophies from C++, Python, and other "traditional" languages. [category: quantum]