Trending repositories

1.numpy / numpy

The fundamental package for scientific computing with Python.

• numpy
• python

2.NVIDIA / cutlass

CUDA Templates and Python DSLs for High-Performance Linear Algebra

• cuda
• deep-learning
• deep-learning-library
• cpp
• nvidia
• gpu
• +1 more

3.XAMPPRocky / tokei

Count your code, quickly.

• tokei
• cloc
• badge
• rust
• windows
• linux
• +6 more

4.Z3Prover / z3

The Z3 Theorem Prover

5.Biohub / esm

The repository host gives no description.

6.isl-org / Open3D

Open3D: A Modern Library for 3D Data Processing

• mesh-processing
• computer-graphics
• opengl
• cpp
• python
• reconstruction
• +14 more

7.sympy / sympy

A computer algebra system written in pure Python

• python
• math
• computer-algebra
• science
• hacktoberfest

8.g-truc / glm

OpenGL Mathematics (GLM)

• glm
• opengl
• mathematics
• vector
• matrix
• quaternion
• +6 more

9.ClawBio / ClawBio

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

• ai-agents
• bioinformatics
• equity
• genomics
• local-first
• openclaw
• +2 more

10.openrocket / openrocket

Model-rocketry aerodynamics and trajectory simulation software

• aerospace
• flight-simulator
• java
• modeling
• optimization
• rocket
• +3 more

11.RosettaCommons / RFdiffusion

Code for running RFdiffusion

12.biopython / biopython

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython
• protein
• protein-structure
• +3 more

13.Slicer / Slicer

Multi-platform, free open source software for visualization and image computing.

• medical-imaging
• vtk
• itk
• python
• qt
• image-processing
• +14 more

14.CGAL / cgal

The public CGAL repository, see the README below

• cgal
• c-plus-plus
• geometry
• algorithms
• library
• cpp
• +11 more

15.shopspring / decimal

Arbitrary-precision fixed-point decimal numbers in Go

• go
• decimals
• precision
• money
• bignumber
• golang

16.chemprop / chemprop

Message Passing Neural Networks for Molecule Property Prediction

• machine-learning
• chemistry
• neural-networks
• drug-discovery

17.facebookresearch / pytorch3d

PyTorch3D is FAIR's library of reusable components for deep learning with 3D data

18.BrunoLevy / geogram

a programming library with geometric algorithms

• graphics-libraries
• graphics-programming
• mesh-generation
• mesh-processing
• geometry-processing

19.KratosMultiphysics / Kratos

Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software. Modularity, extensibility and HPC are the main objectives. Kratos has BSD license and is written in C++ with extensive Python interface.

• kratos
• fem
• dem
• parallel-computing
• openmp
• numerical-methods
• +7 more

20.mborgerding / kissfft

a Fast Fourier Transform (FFT) library that tries to Keep it Simple, Stupid

21.OpenMDAO / OpenMDAO

OpenMDAO repository.

• nasa
• open-source
• framework
• openmdao
• optimization

22.osrf / gazebo_models

Gazebo database of SDF models. This is a predecessor to https://app.gazebosim.org

• gazebo
• simulation
• robot-simulation
• robotics
• gazebosim
• ros
• +4 more

23.SciML / DifferentialEquations.jl

Multi-language suite for high-performance solvers of differential equations and scientific machine learning (SciML) components. Ordinary differential equations (ODEs), stochastic differential equations (SDEs), delay differential equations (DDEs), differential-algebraic equations (DAEs), and more in Julia.

• differential-equations
• differentialequations
• julia
• ode
• sde
• dae
• +14 more

24.dealii / dealii

The development repository for the deal.II finite element library

• finite-elements
• c-plus-plus
• fem
• hpc
• parallel-computing
• scientific-computing
• +1 more

25.brian-team / brian2

Brian is a free, open source simulator for spiking neural networks.

• python
• neuroscience
• science
• differential-equations
• spiking-neural-networks
• biological-simulations
• +5 more

26.stevengj / nlopt

library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization

27.mahmoud / boltons

🔩 Like builtins, but boltons. 250+ constructs, recipes, and snippets which extend (and rely on nothing but) the Python standard library. Nothing like Michael Bolton.

• python
• utilities
• cache
• data-structures
• statistics
• data-science
• +5 more

28.flexible-collision-library / fcl

Flexible Collision Library

• collision
• collision-detection

29.Reference-LAPACK / lapack

LAPACK development repository

• linear-algebra
• lapack
• blas
• lapacke
• linear-equations
• eigenvalues
• +4 more

30.flame / blis

BLAS-like Library Instantiation Software Framework

• blis
• blas
• blas-libraries
• linear-algebra
• linear-algebra-library
• matrix-multiplication
• +8 more

31.instadeepai / nucleotide-transformer

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna
• foundation-models
• transcriptomics
• +1 more

32.mahmoodlab / UNI

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab
• pathology
• uni
• +11 more

33.mlmed / torchxrayvision

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning
• transfer-learning
• dataset
• +13 more

34.symengine / symengine

SymEngine is a fast symbolic manipulation library, written in C++

• math
• computer-algebra
• c-plus-plus

35.3dmol / 3Dmol.js

WebGL accelerated JavaScript molecular graphics library

• molecular-graphics
• molecular-modeling
• computational-biology
• computational-chemistry

36.hjwdzh / QuadriFlow

QuadriFlow: A Scalable and Robust Method for Quadrangulation

• quadriflow
• quad
• remeshing
• quadrangulation
• geometry

37.trilinos / Trilinos

Primary repository for the Trilinos Project

• snl-science-libs
• sandia-national-laboratories
• hpsf
• scientific-computing
• high-performance-computing
• c-plus-plus
• +2 more

38.NetTopologySuite / NetTopologySuite

A .NET GIS solution that is fast and reliable for the .NET platform.

• topology
• nts
• sfs
• c-sharp
• library
• jts
• +1 more

39.CMA-ES / pycma

Python implementation of CMA-ES

40.PixarAnimationStudios / OpenSubdiv

An Open-Source subdivision surface library.

41.nasa / trick

Trick Simulation Environment. Trick provides a common set of simulation capabilities and utilities to build simulations automatically.

42.mahmoodlab / CONCH

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model
• health-informatics
• histopathology
• +9 more

43.hypre-space / hypre

Parallel solvers for sparse linear systems featuring multigrid methods.

• math-physics
• library
• hpc
• radiuss

44.samtools / htslib

C library for high-throughput sequencing data formats

• htslib
• bioinformatics
• sam
• bam
• cram
• vcf
• +2 more

45.firedrakeproject / firedrake

Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)

46.usnistgov / fipy

FiPy is a Finite Volume PDE solver written in Python

• scientific-computing
• scientific-computing-with-python
• phase-field
• materials-science
• partial-differential-equations
• shared-memory-parallel
• +2 more

47.CATIA-Systems / FMPy

Simulate Functional Mock-up Units (FMUs) in Python

• fmi
• python
• fmi-standard

48.libtom / libtommath

LibTomMath is a free open source portable number theoretic multiple-precision integer library written entirely in C.

• mpi
• libtommath
• c
• math
• multi-precision

49.biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel
• standard
• specification
• +11 more

50.fo-dicom / fo-dicom

Fellow Oak DICOM for .NET, .NET Core, Universal Windows, Android, iOS, Mono and Unity

• dicom
• netcore
• medical
• medical-imaging
• dot-net
• c-sharp
• +4 more

51.immunogenomics / harmony

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

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

52.MmgTools / mmg

open source software for bidimensional and tridimensional remeshing

• mesh
• mesh-adaptation
• anisotropic-mesh-adaptation
• isotropic-mesh-adaptation
• mesh-quality-improvement
• surface-improvement
• +11 more

53.dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

54.PetteriAimonen / libfixmath

Cross Platform Fixed Point Maths Library

55.alphaville / optimization-engine

Nonconvex embedded optimization: code generation for fast real-time optimization + ROS support

• embedded-optimization
• nonconvex
• model-predictive-control
• rust-library
• rust
• rust-crate
• +14 more

56.UniMath / UniMath

This rocq library aims to formalize a substantial body of mathematics using the univalent point of view.

• coq
• mathematics
• unimath
• coq-library
• foundations
• rocq
• +1 more

57.rbdl / rbdl

RBDL is a C++ library that contains some essential and efficient rigid body dynamics algorithms such as the Articulated Body Algorithm (ABA) for forward dynamics, Recursive Newton-Euler Algorithm (RNEA) for inverse dynamics, the Composite Rigid Body Algorithm (CRBA) for the efficient computation of the joint space inertia matrix and is also able to compute forward dynamics with external contact constraints and collision impulses. Furthermore it has some basic support for forward and inverse kinematics.

• articulated-body-algorithm
• inverse-dynamics
• forward-dynamics
• multi-body-dynamics
• inverse-kinematics
• robotics

58.rafat / wavelib

C Implementation of 1D and 2D Wavelet Transforms (DWT,SWT and MODWT) along with 1D Wavelet packet Transform and 1D Continuous Wavelet Transform.

• wavelets
• dwt
• continuous-wavelet-transform
• wavelet-packet-trees
• c
• cpp

59.sanderlab / scPerturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

• cite-seq
• database
• perturbation
• scatac-seq
• science
• scrna-seq
• +4 more

60.qhull / qhull

Qhull development for www.qhull.org -- Qhull 2020.2 (8.1-alpha1) at https://github.com/qhull/qhull/wiki

• qhull
• computational-geometry
• convex-hull
• delaunay-triangulation
• voronoi-diagram
• halfspace-intersection
• +3 more

61.rsvp / fecon235

Notebooks for financial economics. Keywords: Jupyter notebook pandas Federal Reserve FRED Ferbus GDP CPI PCE inflation unemployment wage income debt Case-Shiller housing asset portfolio equities SPX bonds TIPS rates currency FX euro EUR USD JPY yen XAU gold Brent WTI oil Holt-Winters time-series forecasting statistics econometrics

• jupyter-notebook
• pandas
• federal-reserve
• gdp
• inflation
• housing
• +14 more

62.brandon-rhodes / pyephem

Scientific-grade astronomy routines for Python

63.prody / ProDy

A Python Package for Protein Dynamics Analysis

• python
• protein
• dynamics

64.chebfun / chebfun

Chebfun: numerical computing with functions.

65.ebassi / graphene

A thin layer of graphic data types

• graphics-library
• vector
• transformations
• matrix
• 3d-transformations
• c
• +4 more

66.rocq-community / fourcolor

Formal proof of the Four Color Theorem [maintainer=@ybertot]

• coq
• ssreflect
• mathcomp
• four-color-theorem
• coq-ci

67.kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny
• single-cell-analysis
• single-cell-rna-seq
• +4 more

68.inducer / meshpy

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

• python
• mesh-generation
• scientific-computing
• triangle
• tetgen
• wrapper
• +1 more

69.excessive / cpml

Cirno's Perfect Math Library: Just about everything you need for 2D/3D games. Hopefully.

• math

70.LigandPro / Matcha

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery
• flowmatching
• gnina
• +8 more

71.PaddlePaddle / Quantum

The repository host gives no description.

72.facebookarchive / prepackArchived

A JavaScript bundle optimizer.

• javascript
• optimization

73.yt-project / yt

Main yt repository

• data
• visualization
• analysis
• python
• scientific-computing
• scientific-visualization
• +6 more

74.neslib / FastMath

Fast Math Library for Delphi

• delphi-rtl
• delphi-fastmath
• fastmath
• overloaded-operators
• vectors
• matrix
• +2 more

75.haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

• python
• protein
• pdb
• bioinformatics
• structural-biology
• structural-bioinformatics
• +2 more

76.lukaszcz / coqhammer

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

• coq
• hammer
• automation
• proof-search
• theorem-prover
• verification
• +3 more

77.HALFpipe / HALFpipe

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

• neuroimaging
• reproducibility
• pipeline
• meta-analysis
• bids
• fmri

78.HIPS / Spearmint

Spearmint Bayesian optimization codebase

79.pschwllr / MolecularTransformer

The repository host gives no description.

80.xiaoyeli / superlu

Supernodal sparse direct solver. https://portal.nersc.gov/project/sparse/superlu/

81.math-comp / analysis

Mathematical Components compliant Analysis Library

• rocq
• analysis
• coq
• mathcomp
• ssreflect

82.dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter
• count-min-sketch
• graph-traversal
• +1 more

83.pymor / pymor

pyMOR - Model Order Reduction with Python

• python
• model-reduction
• model-order-reduction
• control-systems
• state-space
• data-driven
• +8 more

84.JuliaPhylo / PhyloNetworks.jl

PhyloNetworks: a julia package with utilities for phylogenetic networks

85.FunctionLab / sei-framework

code to run sei and obtain sei and sequence class predictions

86.bp-kelley / descriptastorus

Descriptor computation(chemistry) and (optional) storage for machine learning

87.mapbox / wagyu

A general library for geometry operations of union, intersections, difference, and xor

• computational-geometry
• union
• intersection
• xor
• geometry
• difference
• +1 more

88.agemagician / Ankh

Ankh: Optimized Protein Language Model

89.ropensci / rentrez

talk with NCBI entrez using R

• r
• rstats
• r-package

90.xtreemze / defend

Procedural Cross-Platform 3D Tower Defense WebGame with Physics and AI and Procedural Sound

• babylonjs
• javascript
• typescript
• projectiles
• towers

91.rii-mango / Papaya

A pure JavaScript medical research image viewer.

92.OpenSimulationInterface / open-simulation-interface

A generic interface for the environmental perception of automated driving functions in virtual scenarios.

• asam
• osi
• open-simulation-interface
• simulation

93.radsz / jacop

Java Constraint Programming solver

94.CellProfiler / CellProfiler-Analyst

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• cellprofiler-analyst
• cellprofiler
• image-analysis
• machine-learning

95.ekrich / sblas

Scala Native BLAS (Basic Linear Algebra Subprograms) supporting Linux and macOS

• scala
• scala-native
• math
• linear-algebra
• blas
• linux
• +1 more

96.Inochi2D / inmath

Games math library for D

• dlang
• math
• nogc