401.brainglobe / cellfinder
Automated 3D cell detection in very large images
- microscopy
- cell-detection
- deep-learning
- image-analysis
- neuroscience
- python
- +2 more
+3 stars
from 230 · score 1.39
Trending repositories
Ranked by Attention Score: stars gained over the last 90 complete days
401–500 of 547 by Attention Score · Aug 7, 2026 – Nov 4, 2026 (UTC)
402.spatstat / spatstat
Umbrella package of the 'spatstat' family................
- r
- spatial-analysis
- spatial-data
- spatstat
- spatial-data-analysis
- statistics
- +11 more
+3 stars
from 206 · score 1.39
403.mapbox / wagyu
A general library for geometry operations of union, intersections, difference, and xor
- computational-geometry
- union
- intersection
- xor
- geometry
- difference
- +1 more
+3 stars
from 195 · score 1.39
404.akrherz / iem
Code that makes the Iowa Environmental Mesonet run, or run into the ground.
- weather
- mesonet
- iowa
+3 stars
from 193 · score 1.39
+3 stars
from 190 · score 1.39
406.connorcoley / rdchiral
Wrapper for RDKit's RunReactants to improve stereochemistry handling
+3 stars
from 188 · score 1.39
407.mcs07 / MolVS
Molecule Validation and Standardization
- rdkit
- python
- chemistry
- cheminformatics
- standardization
- validation
+3 stars
from 186 · score 1.39
408.txWang / MOGONET
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
+3 stars
from 186 · score 1.39
+3 stars
from 175 · score 1.39
410.nathan-osman / go-sunrise
Go package for calculating the sunrise and sunset times for a given location
+3 stars
from 175 · score 1.39
411.OpenBioLink / OpenBioLink
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
+3 stars
from 161 · score 1.39
412.lifanchen-simm / transformerCPI
TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524
- self-attention
- compound-protein-interaction
- transformercpi
- structure-free-virtual-sreening
- drug-target-identification
- drug-discovery
+3 stars
from 156 · score 1.39
413.brainglobe / brainreg
Automated 3D brain registration with support for multiple species and atlases.
- registration
- atlases
- brain
- neuroscience
- microscopy
- neuroanatomy
+3 stars
from 149 · score 1.39
414.bowang-lab / scGPT-spatial
The repository host gives no description.
+3 stars
from 141 · score 1.39
415.HALFpipe / HALFpipe
ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data
- neuroimaging
- reproducibility
- pipeline
- meta-analysis
- bids
- fmri
+3 stars
from 128 · score 1.39
416.axondeepseg / axondeepseg
Axon/Myelin segmentation using Deep Learning
- deep-learning
- machine-learning
- myelin
- axon
- neuropoly
- spinalcord
- +5 more
+3 stars
from 126 · score 1.39
+3 stars
from 108 · score 1.39
+3 stars
from 65 · score 1.39
419.Nonanti / MathFlow
C# math expression library with symbolic computation support
- csharp
- dotnet
- expression-parser
- math
- mathematics
- symbolic-computation
- +4 more
+3 stars
from 56 · score 1.39
420.RucDongLab / STAGATE
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
+3 stars
from 52 · score 1.39
421.wukevin / babel
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
- multi-omics
+3 stars
from 50 · score 1.39
422.d-SEAMS / seams-core
The d-SEAMS C++ core engine
- molecular-dynamics-simulation
- molecular-dynamics
- trajectory-analysis
- lua
- nix
- d-seams
- +8 more
+3 stars
from 40 · score 1.39
423.myzhengSIMM / TranSiGen
The repository host gives no description.
+3 stars
from 36 · score 1.39
424.cafferychen777 / flashdeconv
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution
- python
- scanpy
- +3 more
+3 stars
from 23 · score 1.39
425.hissain / jscipy
Java Scientific Computing Library - Signal Processing, FFT, Filters, PSD, DCT, SciPy-like APIs for JVM & Android used in Machine Learning and Data Science.
- android
- java
- python
- scipy
- scipy-signal
- signal-processing
- +13 more
+3 stars
from 23 · score 1.39
426.ppissias / SpacePixels
Astronomical FITS image analysis tool for detecting asteroids, comets, satellites, moving objects, and transients in astrophotography data.
- astronomy
- astronomy-software
- astrophotography
- moving-object-detection
- photometry
- variable-stars
- +6 more
+3 stars
from 5 · score 1.39
427.bcbio / bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
+2 stars
from 1,028 · score 1.10
428.romeric / Fastor
A lightweight high performance tensor algebra framework for modern C++
+2 stars
from 842 · score 1.10
429.ZacharyPatten / Towel
Throw in the towel.
- dotnet
- towel
- csharp
- library
- data-structures
- mathematics
- +12 more
+2 stars
from 778 · score 1.10
430.Project-Platypus / Platypus
A Free and Open Source Python Library for Multiobjective Optimization
- optimization
- multiobjective
- evolutionary
- algorithm
- genetic
- python
+2 stars
from 652 · score 1.10
431.heremaps / pptk
The Point Processing Toolkit (pptk) is a Python package for visualizing and processing 2-d/3-d point clouds.
- pointclouds
- 3-d
- visualization
- lidar
- graphics-3d
- gps-data
- +2 more
+2 stars
from 633 · score 1.10
432.ceeK / Solar
A Swift micro library for generating Sunrise and Sunset times on device, requiring no network access.
+2 stars
from 613 · score 1.10
433.wengong-jin / icml18-jtnn
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
+2 stars
from 562 · score 1.10
+2 stars
from 477 · score 1.10
435.pschwllr / MolecularTransformer
The repository host gives no description.
+2 stars
from 427 · score 1.10
436.damienBloch / inkscape-raytracing
An extension for Inkscape that makes it easier to draw optical diagrams.
- inkscape-extension
- optics-simulation
- python
- optics
+2 stars
from 377 · score 1.10
437.MolecularAI / ReinventArchived
The repository host gives no description.
- cheminformatics
- neural-networks
- astrazeneca
- reinforcement-learning
- denovo-design
- transfer-learning
+2 stars
from 376 · score 1.10
438.mathnet / mathnet-symbolics
Math.NET Symbolics
- computer-algebra
- mathnet
- dotnet
- fsharp
- symbolic-manipulation
- math
+2 stars
from 367 · score 1.10
439.pymor / pymor
pyMOR - Model Order Reduction with Python
- python
- model-reduction
- model-order-reduction
- control-systems
- state-space
- data-driven
- +8 more
+2 stars
from 345 · score 1.10
+2 stars
from 342 · score 1.10
441.pbrod / numdifftools
Solve automatic numerical differentiation problems in one or more variables.
+2 stars
from 281 · score 1.10
442.bp-kelley / descriptastorus
Descriptor computation(chemistry) and (optional) storage for machine learning
+2 stars
from 280 · score 1.10
443.Fil / d3-geo-voronoi
Voronoi / Delaunay tessellations on the sphere
- voronoi
- d3js
- d3
- geospatial
- convex-hull
- delaunay-triangulation
+2 stars
from 276 · score 1.10
444.kaapana / kaapana
Kaapana is an open source toolkit for state of the art platform provisioning in the field of medical data analysis. The applications comprise AI-based workflows and federated learning scenarios with a focus on radiological and radiotherapeutic imaging. The name Kaapana comes from the Hawaiian word kaʻāpana, meaning "distributor" or "part".
- imaging
- ai
- cloud-computing
- medical-imaging
- medical-image-processing
- platform
- +1 more
+2 stars
from 274 · score 1.10
+2 stars
from 248 · score 1.10
446.meshpro / dmsh
:spider_web: Simple mesh generator inspired by distmesh.
- mesh
- finite-elements
- mathematics
- mesh-generation
- python
- python3
+2 stars
from 221 · score 1.10
+2 stars
from 219 · score 1.10
448.microsoft / Quantum-NCArchived
Microsoft Quantum Computing Libraries for noncommercial use
- quantum-development-kit
- quantum
- qdk
- quantum-computing
- qsharp
- python
+2 stars
from 209 · score 1.10
449.blender-nlp / MolT5
Associated Repository for "Translation between Molecules and Natural Language"
+2 stars
from 193 · score 1.10
450.mahmoodlab / TOAD
AI-based pathology predicts origins for cancers of unknown primary - Nature
- histology
- pathology
- wsi-images
- histopathology
- cancer-imaging-research
- cancer-research
- +9 more
+2 stars
from 184 · score 1.10
+2 stars
from 179 · score 1.10
452.hachmannlab / chemml
ChemML is a machine learning and informatics program suite for the chemical and materials sciences.
- quantum-mechanics
- materials-informatics
- data-science
- machine-learning
- drug-discovery
- deep-learning
+2 stars
from 178 · score 1.10
453.JuliaPhylo / PhyloNetworks.jl
PhyloNetworks: a julia package with utilities for phylogenetic networks
+2 stars
from 175 · score 1.10
454.PatWalters / rd_filters
A script to run structural alerts using the RDKit and ChEMBL
+2 stars
from 171 · score 1.10
455.CellProfiler / CellProfiler-Analyst
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
+2 stars
from 170 · score 1.10
456.chao1224 / ChatDrug
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
- editing
- molecule
- +11 more
+2 stars
from 161 · score 1.10
+2 stars
from 155 · score 1.10
458.ebi-webcomponents / nightingale
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
- biohackeu22
+2 stars
from 150 · score 1.10
459.cytomining / pycytominer
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
- cellprofiler
- image-analysis
- +1 more
+2 stars
from 144 · score 1.10
460.mrkrd / cochlea
Inner ear models for Python
- python
- cochlea
- inner-ear
- model
- auditory
- computational-neuroscience
- +4 more
+2 stars
from 129 · score 1.10
461.rocq-community / corn
Coq Repository at Nijmegen [maintainers=@spitters,@VincentSe,@Lysxia]
- coq-library
- real-number
- coq
- coq-ci
- coq-platform
+2 stars
from 115 · score 1.10
462.angelolab / ark-analysis
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
+2 stars
from 108 · score 1.10
463.JuliaGraphs / NetworkLayout.jl
Layout algorithms for graphs and trees in pure Julia.
- graph-visualization
+2 stars
from 107 · score 1.10
464.OpenTire / OpenTirePython
An open-source mathematical tire modelling library
+2 stars
from 66 · score 1.10
465.SuperBianC / scMulan
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
+2 stars
from 62 · score 1.10
+2 stars
from 58 · score 1.10
467.gistrec / geo-utils-cpp
Tiny header-only C++17 library for lat/lng geometry: distance, bearing, area, point-in-polygon and path proximity
- cpp
- geometry
- geospatial
- gis
- gps
- haversine
- +9 more
+2 stars
from 53 · score 1.10
468.hamaluik / haxe-glm
Native Haxe functions for graphical linear algebra (à la GLM: https://github.com/g-truc/glm/tree/master/glm)
+2 stars
from 46 · score 1.10
469.rocq-community / graph-theory
Graph Theory [maintainers=@chdoc,@damien-pous]
- coq
- graph-theory
- mathcomp
- docker-coq-action
- mathcomp-ci
+2 stars
from 44 · score 1.10
470.chrissnell / remoteweather
A weather server supporting Campbell Scientific and Davis Instruments stations with lots of data-sharing options
+2 stars
from 32 · score 1.10
471.BoevaLab / CancerFoundation
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
- cancer
- foundation-model
- single-cell
+2 stars
from 30 · score 1.10
472.sebsjames / maths
C++ modules for scalar, vector and complex math. And maths.
- cpp20
- math
- mathematics
- vectors
- matrix
- transform
- +3 more
+2 stars
from 9 · score 1.10
473.kslamph / tronlib
A production-ready Go SDK for TRON: gRPC client with connection pooling, HD wallets, TRC-10/TRC-20, event decoding, transaction simulation, and shielded TRC-20 (Sapling) support. 85% test coverage.
- blockchain
- cryptocurrency
- go
- golang
- sdk
- smart-contracts
- +14 more
+2 stars
from 4 · score 1.10
474.kVeyra / sklearn-java
Java reimplementation of Python's scikit-learn with behavioral compatibility, numerical accuracy, and idiomatic Java design
+2 stars
from 3 · score 1.10
475.cornerstonejs / cornerstone
[Deprecated] Use Cornerstone3D Instead https://cornerstonejs.org/
- javascript
- cornerstone
- dicom
- medical-imaging
- nci-itcr
+1 stars
from 2,105 · score 0.69
+1 stars
from 1,029 · score 0.69
477.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
+1 stars
from 788 · score 0.69
478.ddemidov / vexcl
VexCL is a C++ vector expression template library for OpenCL/CUDA/OpenMP
- opencl
- cuda
- c-plus-plus
- gpgpu
- scientific-computing
- cpp11
+1 stars
from 721 · score 0.69
479.jhomlala / feather
Flutter weather application with beautiful UI and UX.
+1 stars
from 690 · score 0.69
480.moble / quaternion
Add built-in support for quaternions to numpy
+1 stars
from 658 · score 0.69
481.DiffSharp / DiffSharp
DiffSharp: Differentiable Functional Programming
- machine-learning
- tensor
- dotnet
- autodiff
- gpu
- deep-learning
- +1 more
+1 stars
from 615 · score 0.69
+1 stars
from 608 · score 0.69
+1 stars
from 600 · score 0.69
484.100 / Solid
🎯 A comprehensive gradient-free optimization framework written in Python
- metaheuristics
- optimization
- optimization-algorithms
- python
- algorithm
- library
- +14 more
+1 stars
from 582 · score 0.69
485.anassinator / ilqr
Iterative Linear Quadratic Regulator with auto-differentiatiable dynamics models
- trajectory-optimization
- differential-dynamic-programming
- theano
- dynamics-models
- auto-differentiation
- model-predictive-control
- +12 more
+1 stars
from 423 · score 0.69
486.OpenSimulationInterface / open-simulation-interface
A generic interface for the environmental perception of automated driving functions in virtual scenarios.
- asam
- osi
- open-simulation-interface
- simulation
+1 stars
from 299 · score 0.69
487.samoturk / mol2vecArchived
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
- python
- machine-learning
- cheminformatics
+1 stars
from 293 · score 0.69
488.fundamentalslib / fundamentals5
Fundamentals 5 Code Library for FreePascal and Delphi
+1 stars
from 276 · score 0.69
489.GPflow / GPflowOpt
Bayesian Optimization using GPflow
- gpflow
- bayesian-optimization
- machine-learning
- hyperparameter-optimization
+1 stars
from 275 · score 0.69
490.statebox / idris-ct
formally verified category theory library
- category-theory
- formal-verification
- formal-proofs
+1 stars
from 272 · score 0.69
491.quil-lang / magicl
Matrix Algebra proGrams In Common Lisp.
- common-lisp
- matrix-algebra
- linear-algebra
+1 stars
from 255 · score 0.69
492.go-hep / hepArchived
hep is the mono repository holding all of go-hep.org/x/hep packages and tools
- golang
- go
- hep
- go-hep
- lhc
- xrootd
- +9 more
+1 stars
from 253 · score 0.69
493.DICOMcloud / DICOMcloud
Azure friendly DICOMweb part 18 .NET server with qido-rs, wado-rs, stow-rs, wado-uri RESTful implementation
- dicom
- dicomweb
- dicomcloud
- wado
- wado-uri
- wado-rs
- +5 more
+1 stars
from 234 · score 0.69
+1 stars
from 234 · score 0.69
+1 stars
from 223 · score 0.69
496.m-a-d-n-e-s-s / madness
Multiresolution Adaptive Numerical Environment for Scientific Simulation
+1 stars
from 220 · score 0.69
+1 stars
from 211 · score 0.69
498.GeoCoq / GeoCoq
A formalization of geometry in Coq based on Tarski's axiom system
+1 stars
from 209 · score 0.69
499.CBICA / CaPTk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
- cancer-imaging-research
- radiomics
- radiomics-features
- machine-learning
- cpp
- cpp11
- +14 more
+1 stars
from 197 · score 0.69
+1 stars
from 196 · score 0.69