Trending repositories

201.mdolab / OpenAeroStruct

OpenAeroStruct is a lightweight tool that performs aerostructural optimization using OpenMDAO.

• openmdao
• optimization
• aerodynamics
• open-source

202.KangBoming / BulkFormer

BulkFormer: A large-scale foundation model for human bulk transcriptomes

203.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

204.sgorsten / linalg

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

205.ddemidov / amgcl

C++ library for solving large sparse linear systems with algebraic multigrid method

• amg
• c-plus-plus
• sparse-linear-systems
• opencl
• cuda
• gpgpu
• +6 more

206.LiangliangNan / PolyFit

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

• surface-reconstruction
• urban-modeling
• urban-reconstruction
• primitive-extraction
• piecewise-planar-object
• sharp-feature
• +2 more

207.JCash / voronoi

A C implementation for creating 2D Voronoi/Delauney diagrams

208.chainer / chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

• deep-learning
• chemistry
• neural-network
• biology
• chainer
• python
• +1 more

209.microsoft / evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

210.gao-lab / GLUE

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

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

211.brandon-rhodes / python-sgp4

Python version of the SGP4 satellite position library

212.cclib / cclib

Parsers and algorithms for computational chemistry logfiles

• python
• computational-chemistry
• quantum-chemistry

213.biomap-research / scFoundation

The repository host gives no description.

214.DLR-SC / tigl

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

• opencascade
• aircraft
• c-plus-plus
• geometry
• b-spline
• cpacs
• +1 more

215.fish-quant / big-fish

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish
• spatial-features
• spot-detection

216.datenwolf / linmath.h

a lean linear math library, aimed at graphics programming. Supports vec3, vec4, mat4x4 and quaternions

217.nschloe / pygmsh

:spider_web: Gmsh for Python

• python
• pypi
• mesh-generation
• engineering
• mathematics
• meshing

218.PetteriAimonen / libfixmath

Cross Platform Fixed Point Maths Library

219.jerryji1993 / DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu
• sequence
• genome
• +4 more

220.epam / Indigo

Universal cheminformatics toolkit, utilities and database search tools

• indigo
• bingo
• cheminformatics
• chemistry
• python
• dotnet
• +9 more

221.mlange-42 / ark

Ark -- Archetype-based Entity Component System (ECS) for Go.

• ecs
• entity-component-system
• go
• golang
• agent-based-modeling
• gamedev
• +2 more

222.kexinhuang12345 / MolTrans

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

223.MikeMcl / bignumber.js

A JavaScript library for arbitrary-precision decimal and non-decimal arithmetic

• bignumber
• javascript
• arbitrary-precision
• decimal-places
• bigdecimal

224.spatie / laravel-analytics

A Laravel package to retrieve pageviews and other data from Google Analytics

• laravel
• php
• analytics
• google
• statistics

225.Habrador / Computational-geometry

Computational Geometry Unity library with implementations of intersection algorithms, triangulations like delaunay, voronoi diagrams, polygon clipping, bezier curves, ear clipping, convex hulls, mesh simplification, etc

• unity3d
• computational-geometry
• voronoi
• intersections
• convex-hull
• polygon-clipping
• +14 more

226.molecularsets / moses

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

• machine-learning
• generative-models
• drug-discovery
• benchmark

227.libMesh / libmesh

libMesh github repository

• fem
• finite-element-methods
• simulation
• parallel
• amr
• finite-element-analysis
• +2 more

228.immunogenomics / harmony

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

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

229.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

230.esa / pygmo2

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
• evolutionary-algorithms
• multiobjective-optimization
• +9 more

231.BenevolentAI / guacamol

Benchmarks for generative chemistry

232.MAGICS-LAB / DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

• dataset
• dna
• dna-processing
• dna-training
• genome
• genome-analysis
• +10 more

233.esa / pykep

PyKEP is a scientific library providing basic tools for research in interplanetary trajectory design.

• interplanetary
• mission-analysis
• astrodynamics
• aerospace

234.SoloByte / godot-polygon2d-fracture

A simple script for fracturing polygons. Also adds nice helper functions for polygons like calculateArea, triangulate, getRandomPointsInPolygon, getBoundingRect)

• gdscript
• polygon2d-fracture
• godot-engine
• godot
• polygon-triangulation
• gamedev-library
• +7 more

235.CEED / libCEED

CEED Library: Code for Efficient Extensible Discretizations

• ceed
• high-order
• exascale-computing
• api
• ecp
• high-performance-computing
• +5 more

236.marcpinet / citracer

💬 Trace citation chains for any concept across research papers and render them as an interactive graph.

• academic-research
• bibliography
• citation-graph
• cli
• grobid
• literature-review
• +5 more

237.ljvmiranda921 / pyswarms

A research toolkit for particle swarm optimization in Python

• particle-swarm-optimization
• optimization-tools
• pso
• global-optimization
• swarm-intelligence
• machine-learning
• +5 more

238.msteinbeck / tinyspline

ANSI C library for NURBS, B-Splines, and Bézier curves with interfaces for C++, C#, D, Go, Java, Javascript, Lua, Octave, PHP, Python, R, and Ruby.

• nurbs
• b-splines
• bezier-curves
• splines

239.ASC-Community / AngouriMath

Open-source cross-platform symbolic algebra library for C# and F#. Can be used for both production and research purposes.

• csharp
• algebra
• integration
• latex
• parsing
• solver
• +13 more

240.Mariewelt / OpenChem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

• computational-chemistry
• computational-biology
• deep-learning
• deep-neural-networks
• graph-convolutional-networks
• drug-discovery
• +5 more

241.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

242.pyamg / pyamg

Algebraic Multigrid Solvers in Python

• amg
• solver
• python
• multigrid
• sparse-matrix
• pyamg
• +2 more

243.Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library
• c-plus-plus
• alignment-path
• +2 more

244.dicoogle / dicoogle

Dicoogle - Open Source PACS

• dicoogle
• dicom
• pacs
• medical-imaging
• medical-image-computing
• medical-informatics
• +7 more

245.theislab / scvelo

RNA Velocity generalized through dynamical modeling

246.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

247.mordred-descriptor / mordred

a molecular descriptor calculator

248.theislab / scib

Benchmarking analysis of data integration tools

249.architecture-building-systems / CityEnergyAnalyst

City Energy Analyst (CEA) is an open-source urban building energy modeling (UBEM) platform and computation tool for the design of low-carbon and highly efficient cities.

• python
• urban-design
• urban-analytics
• ubem
• open-source
• decarbonization
• +5 more

250.calico / borzoi

RNA-seq prediction with deep convolutional neural networks.

251.biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology

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

252.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

253.theislab / nicheformer

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

254.mreineck / pocketfft

Fork of https://gitlab.mpcdf.mpg.de/mtr/pocketfft to simplify external contributions

255.zcang / COMMOT

The repository host gives no description.

256.weigertlab / spotiflow

Accurate and efficient spot detection for microscopy data

257.Durenlab / LINGER

The repository host gives no description.

258.markrogoyski / math-php

Powerful modern math library for PHP: Features descriptive statistics and regressions; Continuous and discrete probability distributions; Linear algebra with matrices and vectors, Numerical analysis; special mathematical functions; Algebra

• math
• mathematics
• linear-algebra
• statistics
• matrix
• probability
• +11 more

259.cpmech / gosl

Linear algebra, eigenvalues, FFT, Bessel, elliptic, orthogonal polys, geometry, NURBS, numerical quadrature, 3D transfinite interpolation, random numbers, Mersenne twister, probability distributions, optimisation, differential equations.

• scientific-computing
• linear-algebra
• differential-equations
• sparse-systems
• parallel-computations
• computational-geometry
• +6 more

260.rigetti / pyquil

A Python library for quantum programming using Quil.

• forest
• quil
• quantum-computing
• quantum-programming

261.agemagician / ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

262.python-adaptive / adaptive

:chart_with_upwards_trend: Adaptive: parallel active learning of mathematical functions

• adaptive-learning
• machine-learning
• python
• live-plots
• parallel-computing
• adaptive-sampling
• +3 more

263.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

264.brandon-rhodes / pyephem

Scientific-grade astronomy routines for Python

265.yixuan / spectra

A header-only C++ library for large scale eigenvalue problems

• eigenvalues
• arpack
• linear-algebra
• spectra
• header-only

266.HazyResearch / hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

• foundation-models
• genomics
• language-models

267.Yixin-Hu / TetWild

Robust Tetrahedral Meshing in the Wild.

• geometry-processing
• tetrahedral-meshing
• surface-repair
• 3d-triangulation

268.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

269.openslide / openslide

C library for reading virtual slide images

• pathology
• whole-slide-imaging
• c

270.MolSSI / cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

• cookiecutter
• python-packages
• molecular-sciences
• conda-environment
• pytest
• conda-forge
• +2 more

271.tequilahub / tequila

A High-Level Abstraction Framework for Quantum Algorithms

272.ebassi / graphene

A thin layer of graphic data types

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

273.theislab / scarches

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration
• batch-correction
• multimodal-deep-learning
• +4 more

274.lilab-stanford / MUSK

The repository host gives no description.

275.peterstace / simplefeatures

Simple Features is a pure Go Implementation of the OpenGIS Simple Feature Access Specification

• postgis
• spatial-analysis
• gis
• go
• golang
• geometry
• +4 more

276.ElliotXie / CASSIA

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering
• retrieved-augmented-generation
• singlecell
• +7 more

277.shmlkv / dna-claude-analysis

Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.

• analysis
• claude
• claudecode
• dna
• genome

278.clean-css / clean-css

Fast and efficient CSS optimizer for node.js and the Web

• css
• minification
• optimization
• css-optimizations
• css-optimizer
• clean-css

279.giacomelli / GeneticSharp

GeneticSharp is a fast, extensible, multi-platform and multithreading C# Genetic Algorithm library that simplifies the development of applications using Genetic Algorithms (GAs).

• genetic-algorithms
• artificial-intelligence
• c-sharp
• dotnet
• dotnet-core
• dotnet-standard
• +3 more

280.vcflib / vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

• variant-calling
• genomics
• vcf-manipulation
• genotyping
• haplotypecaller

281.inducer / meshpy

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

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

282.aertslab / SCENIC

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

283.shenwei356 / taxonkit

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
• lca
• taxid
• +2 more

284.Dana-Farber-AIOS / pathml

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing
• pathology
• histopathology
• +9 more

285.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

286.quagmt / udecimal

A high-performance, high precision, zero allocation fixed-point decimal library for financial applications

• golang
• high-performance
• zero-allocation
• money
• go
• financial
• +2 more

287.ImagingDataCommons / slim

Interoperable web-based DICOM slide microscopy viewer and annotation tool

• dicomweb
• oidc
• react
• digital-pathology
• idc-viewers

288.vlang / vtl

The V Tensor Library

• v
• hacktoberfest
• autograd
• deep-learning
• linear-algebra
• machine-learning
• +5 more

289.cantinilab / scPRINT

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising
• embeddings
• gene-regulatory-network
• +12 more

290.kreshuklab / panseg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network
• bioimage-analysis
• image-segmentation
• +1 more

291.Perturbation-Response-Prediction / PRnet

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

292.scikit-optimize / scikit-optimizeArchived

Sequential model-based optimization with a `scipy.optimize` interface

• bayesopt
• optimization
• scientific-computing
• machine-learning
• hyperparameter
• bayesian-optimization
• +9 more

293.fcambus / ansiweather

Weather in terminal, with ANSI colors and Unicode symbols

• weather
• terminal
• ansi
• unicode

294.broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

• workflow-execution
• workflow
• cloud
• hpc
• bioinformatics
• executor
• +7 more

295.rawify / Fraction.js

The RAW rational numbers library written in JavaScript

• fraction
• javascript
• math
• rational-numbers
• numbers

296.acado / acado

ACADO Toolkit is a software environment and algorithm collection for automatic control and dynamic optimization. It provides a general framework for using a great variety of algorithms for direct optimal control, including model predictive control, state and parameter estimation and robust optimization.

297.prody / ProDy

A Python Package for Protein Dynamics Analysis

• python
• protein
• dynamics

298.BMIRDS / deepslide

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis
• resnet
• wsi
• +3 more

299.guanjq / targetdiff

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

• ai-for-science
• diffusion-models
• drug-design
• equivariant-networks
• iclr2023

300.hkmztrk / DeepDTA

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks