Trending repositories

201.immunogenomics / harmony

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

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

202.hms-dbmi / viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

• hubmap
• imaging
• openmicroscopy
• ome-tiff
• zarr
• viv
• +1 more

203.KangBoming / BulkFormer

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

204.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

205.datenwolf / linmath.h

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

206.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

207.auto-differentiation / xad

The fastest automatic differentiation library for C++, with Python bindings. Forward, adjoint and higher-order derivatives, checkpointing, Eigen support and JIT. Reproducible benchmarks against CppAD, Adept and autodiff.

• automatic-differentiation
• aad
• algorithmic-differentiation
• autodiff
• adjoint
• cpp
• +13 more

208.cclib / cclib

Parsers and algorithms for computational chemistry logfiles

• python
• computational-chemistry
• quantum-chemistry

209.mdolab / OpenAeroStruct

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

• openmdao
• optimization
• aerodynamics
• open-source

210.dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

211.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.

212.PetteriAimonen / libfixmath

Cross Platform Fixed Point Maths Library

213.yixuan / spectra

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

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

214.biomap-research / scFoundation

The repository host gives no description.

215.Rolf-Hempel / PlanetarySystemStacker

Produce a sharp image of a planetary system object (moon, sun, planets) from many seeing-affected frames according to the "lucky imaging" technique.

216.golang / geo

S2 geometry library in Go

• go
• geometry
• geometry-library
• sphere

217.esa / pykep

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

• interplanetary
• mission-analysis
• astrodynamics
• aerospace

218.microsoft / evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

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

219.softwareQinc / qpp

Modern C++ quantum computing library

• quantum-computing
• c-plus-plus
• cpp
• cpp11
• quantum
• simulator
• +2 more

220.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

221.HazyResearch / hyena-dna

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

• foundation-models
• genomics
• language-models

222.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

223.datamol-io / datamol

Molecular Processing Made Easy.

• python
• molecule
• rdkit
• drug-discovery
• drug-design
• molecules
• +2 more

224.epam / Indigo

Universal cheminformatics toolkit, utilities and database search tools

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

225.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

226.openslide / openslide

C library for reading virtual slide images

• pathology
• whole-slide-imaging
• c

227.gao-lab / GLUE

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

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

228.brandon-rhodes / python-sgp4

Python version of the SGP4 satellite position library

229.theislab / scib

Benchmarking analysis of data integration tools

230.shmlkv / dna-claude-analysis

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

• analysis
• claude
• claudecode
• dna
• genome

231.sgorsten / linalg

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

232.jwiegley / category-theory

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

• category-theory
• coq
• monad
• profunctor
• comonads
• monoid
• +7 more

233.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

234.BenevolentAI / guacamol

Benchmarks for generative chemistry

235.weigertlab / spotiflow

Accurate and efficient spot detection for microscopy data

236.J-SNACKKB / FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

• protein
• protein-sequences
• protein-design
• representation-learning
• protein-fitness-prediction
• protein-function-prediction

237.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

238.chainer / chainer-chemistry

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

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

239.jarun / bcal

:1234: Bits, bytes and general-purpose calculator

• storage
• storage-unit-converter
• command-line
• standalone
• terminal
• calculator
• +6 more

240.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

241.NGSolve / netgen

The repository host gives no description.

• mesh-generator

242.lilab-stanford / MUSK

The repository host gives no description.

243.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

244.spatie / laravel-analytics

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

• laravel
• php
• analytics
• google
• statistics

245.rigetti / pyquil

A Python library for quantum programming using Quil.

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

246.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

247.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

248.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

249.bjodah / chempy

⚗ A package useful for chemistry written in Python

• chemistry
• physical-chemistry
• chemical-kinetics
• chemical-formulas
• chemical-reaction-model
• python
• +1 more

250.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

251.kuleshov-group / caduceus

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

252.kexinhuang12345 / MolTrans

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

253.mreineck / pocketfft

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

254.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

255.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

256.hms-dbmi / CHIEF

Clinical Histopathology Imaging Evaluation Foundation Model

257.theislab / scvelo

RNA Velocity generalized through dynamical modeling

258.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

259.tequilahub / tequila

A High-Level Abstraction Framework for Quantum Algorithms

260.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

261.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

262.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

263.theislab / nicheformer

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

264.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

265.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

266.nschloe / pygmsh

:spider_web: Gmsh for Python

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

267.pyamg / pyamg

Algebraic Multigrid Solvers in Python

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

268.aertslab / SCENIC

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

269.CEED / libCEED

CEED Library: Code for Efficient Extensible Discretizations

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

270.cantinilab / scPRINT

🏃 The go-to single-cell Foundation Model

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

271.scikit-optimize / scikit-optimizeArchived

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

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

272.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

273.libMesh / libmesh

libMesh github repository

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

274.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.

275.zcang / COMMOT

The repository host gives no description.

276.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

277.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

278.brandon-rhodes / pyephem

Scientific-grade astronomy routines for Python

279.bebop / poly

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology
• bioengineering
• computational-biology
• +14 more

280.Yixin-Hu / TetWild

Robust Tetrahedral Meshing in the Wild.

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

281.prody / ProDy

A Python Package for Protein Dynamics Analysis

• python
• protein
• dynamics

282.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

283.mordred-descriptor / mordred

a molecular descriptor calculator

284.clean-css / clean-css

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

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

285.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

286.bigdatagenomics / adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics
• parquet
• avro
• +4 more

287.chebfun / chebfun

Chebfun: numerical computing with functions.

288.dicoogle / dicoogle

Dicoogle - Open Source PACS

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

289.Dana-Farber-AIOS / pathml

Tools for computational pathology

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

290.ebassi / graphene

A thin layer of graphic data types

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

291.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

292.thinng / GraphDTA

GraphDTA: Predicting drug-target binding affinity with graph neural networks

293.rocq-community / fourcolor

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

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

294.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

295.fish-quant / big-fish

Toolbox for the analysis of smFISH images.

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

296.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

297.sqjin / CellChatArchived

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

• cell-cell-communication
• single-cell-analysis
• cell-cell-interaction
• microenvironment

298.inducer / meshpy

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

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

299.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

300.MolSSI / cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

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