JOSS collection | Ecosyste.ms: Summary

https://github.com/tidymodels/stacks

An R package for tidy stacked ensemble modeling

Last synced: 12 Aug 2026

https://github.com/koide3/small_gicp

Efficient and parallel algorithms for point cloud registration [C++, Python]

cpp icp multi-threading open3d pcl point-cloud-regstration pointcloud python registration scan-matching

Last synced: 13 Aug 2026

https://github.com/cgre-aachen/gemgis

Spatial data processing for geomodeling

geographic geographic-data geomodeling geospatial jupyter jupyter-notebook modeling notebooks processing python raster-data spatial-data vector-data visualization

Last synced: 12 Aug 2026

https://github.com/onecodex/finch-rs

A genomic minhashing implementation in Rust

Last synced: 13 Aug 2026

https://github.com/lantunes/cellpylib

A library for working with Cellular Automata, for Python.

cellular-automata complex-systems complexity computation nonlinear-dynamics

Last synced: 13 Aug 2026

https://github.com/Pometry/Raphtory

Scalable graph analytics database powered by a multithreaded, vectorized temporal engine, written in Rust

analytics database embedded-database graph graph-database olap python rust temporal time-series

Last synced: 13 Aug 2026

https://github.com/ropensci/tidyhydat

An R package to import Water Survey of Canada hydrometric data and make it tidy

citz government-data hydrology hydrometrics r r-package rstats tidy-data water-resources

Last synced: 13 Aug 2026

https://github.com/hiddenSymmetries/simsopt

Simons Stellarator Optimizer Code

fusion nuclear-fusion optimization plasma plasma-physics stellarator stellarators

Last synced: 13 Aug 2026

https://github.com/dib-lab/khmer

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

bioinformatics bloom-filter count-min-sketch dna graph-traversal k-mer python

Last synced: 13 Aug 2026

https://github.com/mathLab/EZyRB

Easy Reduced Basis method

autoencoder data-driven hacktoberfest model-order-reduction model-reduction non-intrusive-model-order-reduction pod-gpr pod-interpolation pod-nn proper-orthogonal-decomposition reduced-basis

Last synced: 13 Aug 2026

https://github.com/ECSHackWeek/impedance.py

A Python package for working with electrochemical impedance data

battery corrosion electrochemistry fuel-cell impedance lithium-ion

Last synced: 13 Aug 2026

https://github.com/mne-tools/mne-icalabel

Automatic labeling of ICA components in Python.

eeg ica neuroscience python

Last synced: 13 Aug 2026

https://github.com/gridap/Gridap.jl

Grid-based approximation of partial differential equations in Julia

finite-elements gridap julia numerical-methods partial-differential-equations pdes

Last synced: 13 Aug 2026

https://github.com/juanmc2005/diart

A python package to build AI-powered real-time audio applications

deep-learning real-time speaker-diarization speaker-embedding streaming-audio transcription voice-activity-detection

Last synced: 13 Aug 2026

https://github.com/xanaduAI/thewalrus

A library for the calculation of hafnians, Hermite polynomials and Gaussian boson sampling.

algorithm combinatorics graphs matrix optimization physics quantum quantum-computing

Last synced: 13 Aug 2026

https://github.com/vc1492a/PyNomaly

Anomaly detection using LoOP: Local Outlier Probabilities, a local density based outlier detection method providing an outlier score in the range of [0,1].

anomalies anomaly-detection machine-learning nearest-neighbors outlier-detection outlier-scores outliers probability

Last synced: 13 Aug 2026

https://github.com/vanheeringen-lab/genomepy

genes and genomes at your fingertips

bioconda ensembl genome ncbi python ucsc

Last synced: 13 Aug 2026

https://github.com/AlexanderFabisch/gmr

Gaussian Mixture Regression

gaussian-mixture-models machine-learning python regression

Last synced: 12 Aug 2026

https://github.com/UW-Hydro/MetSim

Meteorology Simulator

climate disaggregation hydrology meteorology mtclim

Last synced: 13 Aug 2026

https://github.com/OpenMDAO/dymos

Open Source Optimization of Dynamic Multidisciplinary Systems

co-design nasa openmdao optimal-control pseudospectral trajectory-optimization

Last synced: 13 Aug 2026

https://github.com/SDXorg/pysd

System Dynamics Modeling in Python

Last synced: 13 Aug 2026

https://github.com/pymedphys/pymedphys

A community effort to develop an open standard library for Medical Physics in Python. Building quality transparent software together via peer review and open source distribution. Open code is better science.

dicom medical-physics radiation-oncology radiation-physics radiation-therapy radiotherapy

Last synced: 13 Aug 2026

https://github.com/zillow/quantile-forest

Quantile Regression Forests compatible with scikit-learn.

machine-learning prediction-intervals python quantile-regression quantile-regression-forests random-forest scikit-learn-api uncertainty-estimation

Last synced: 12 Aug 2026

https://github.com/dhermes/bezier

Helper for Bézier Curves, Triangles, and Higher Order Objects

Last synced: 13 Aug 2026

https://github.com/flekschas/regl-scatterplot

Scalable WebGL-based scatter plot library build with Regl

2d regl scatter-plot scatterplot visualization webgl

Last synced: 12 Aug 2026

https://github.com/sunpy/drms

Access HMI, AIA and MDI data with Python from public JSOC DRMS servers

Last synced: 13 Aug 2026

https://github.com/CLIMADA-project/climada_python

CLIMADA is a free and open-source software framework for climate risk assessment and adaptation option appraisal.

Last synced: 13 Aug 2026

https://github.com/SMTG-Bham/doped

doped is a Python software for the generation, pre-/post-processing and analysis of defect supercell calculations, implementing the defect simulation workflow in an efficient, reproducible, user-friendly yet powerful and fully-customisable manner.

ab-initio computational-chemistry computational-materials-science defect-calculation defect-formation-energy defect-levels defect-thermodynamics defects dft doping fermi-level point-defects pymatgen semiconductors shakenbreak transition-levels vasp

Last synced: 12 Aug 2026

https://github.com/ME-ICA/tedana

TE-dependent analysis of multi-echo fMRI

brain-imaging fmri neuroimaging python

Last synced: 13 Aug 2026

https://github.com/vmagnin/gtk-fortran

A GTK / Fortran binding, and its documentation (in the Wiki tab).

bindings cross-platform fortran fortran-package-manager graphical-user-interface graphics gtk gtk-fortran gtk4 gui

Last synced: 13 Aug 2026

https://github.com/ropensci/rdataretriever

R interface to the Data Retriever

data data-science database datasets r r-package rstats science

Last synced: 13 Aug 2026

https://github.com/JuliaGeometry/DelaunayTriangulation.jl

DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane

computational-geometry delaunay delaunay-triangulation geometry meshing power-diagram tessellation triangulation voronoi voronoi-diagram

Last synced: 12 Aug 2026

https://github.com/xCDAT/xcdat

An extension of xarray for climate data analysis on structured grids.

cdat cf-conventions climate-analysis climate-data climate-data-analysis climate-research climate-science climate-sciences cmip cmip6 e3sm earth-system earth-system-data earth-system-science pcmdi python xarray xcdat

Last synced: 13 Aug 2026

https://github.com/FitSNAP/FitSNAP

Software for generating machine-learning interatomic potentials for LAMMPS

Last synced: 13 Aug 2026

https://github.com/JuliaManifolds/Manopt.jl

🏔️Optimization on Riemannian Manifolds in Julia

julia manifolds manopt optimization

Last synced: 13 Aug 2026

https://github.com/rgerum/pylustrator

Visualisations of data are at the core of every publication of scientific research results. They have to be as clear as possible to facilitate the communication of research. As data can have different formats and shapes, the visualisations often have to be adapted to reflect the data as well as possible. We developed Pylustrator, an interface to directly edit python generated matplotlib graphs to finalize them for publication. Therefore, subplots can be resized and dragged around by the mouse, text and annotations can be added. The changes can be saved to the initial plot file as python code.

code-generation gui interactive matplotlib visualisation

Last synced: 13 Aug 2026

https://github.com/nifty-ppl/nifty

Probabilistic programming framework for signal inference algorithms that operate regardless of the underlying grids and their resolutions

Last synced: 12 Aug 2026

https://github.com/stingraysoftware/stingray

Anything can happen in the next half hour (including spectral timing made easy)!

astronomy astrophysics blackhole blackholes data-analysis fourier-analysis fourier-transform hacktoberfest neutronstars pulsars time-series time-series-analysis timeseries x-ray x-ray-binaries

Last synced: 13 Aug 2026

https://github.com/StingraySoftware/stingray

Anything can happen in the next half hour (including spectral timing made easy)!

astronomy astrophysics blackhole blackholes data-analysis fourier-analysis fourier-transform hacktoberfest neutronstars pulsars time-series time-series-analysis timeseries x-ray x-ray-binaries

Last synced: 13 Aug 2026

https://github.com/SuperKogito/spafe

:sound: spafe: Simplified Python Audio Features Extraction

audio audio-analysis beat dsp features-extraction filterbank frequencies frequency frequency-analysis gammatone-filterbanks mfcc music music-information-retrieval pitch python signal-processing sound speech-processing time-frequency-analysis voice

Last synced: 13 Aug 2026

https://github.com/salabim/salabim

salabim - discrete event simulation

animation discrete-event-simulation logistics python

Last synced: 13 Aug 2026

https://github.com/esa/polyhedral-gravity-model

Implementation of a polyhedral gravity model in C++17 with a Python Binding

cpp17 gravity polyhedral-model python

Last synced: 12 Aug 2026

https://github.com/JunoLab/Weave.jl

Scientific reports/literate programming for Julia

julia literate-programming reproducible-research scientific-reports scientific-workflows

Last synced: 13 Aug 2026

https://github.com/gadomski/antimeridian

Correct GeoJSON geometries that cross the 180th meridian

antimeridian geojson geospatial python

Last synced: 12 Aug 2026

https://github.com/weecology/retriever

Quickly download, clean up, and install public datasets into a database management system

data data-retrieval data-science dataset datasets hacktobefest python

Last synced: 13 Aug 2026

https://github.com/dit/dit

Python package for information theory.

information-theory python

Last synced: 13 Aug 2026

https://github.com/ropensci/ezknitr

Avoid the typical working directory pain when using 'knitr'

knitr peer-reviewed r r-package reproducibility rmarkdown rmd rstats

Last synced: 13 Aug 2026

https://github.com/siavashk/pycpd

Pure Numpy Implementation of the Coherent Point Drift Algorithm

expectation-maximization point-cloud python registration

Last synced: 13 Aug 2026

https://github.com/shirtsgroup/physical_validation

Physical validation of molecular simulations

molecular-dynamics molecular-mechanics molecular-simulation physical-validation python

Last synced: 12 Aug 2026

https://github.com/NASA-Planetary-Science/sbpy

A Python package for small bodies research

asteroids astronomy comets research

Last synced: 13 Aug 2026

https://github.com/jacksund/simmate

Simmate: a full-stack framework for chemistry research.

Last synced: 13 Aug 2026

https://github.com/bihealth/vcfpy

Python 3 library with good support for both reading and writing VCF

bioinformatics file-format parsing vcf writing

Last synced: 13 Aug 2026

https://github.com/carlganz/rintrojs

Wrapper for the Intro.js library

cran introjs r shiny

Last synced: 13 Aug 2026

https://github.com/chasmani/piecewise-regression

piecewise-regression (aka segmented regression) in python. For fitting straight line models to data with one or more breakpoints where the gradient changes.

data-analysis linear-regression model-fitting piecewise-regression python3 regression segmented-regression statistics

Last synced: 12 Aug 2026

https://github.com/data-edu/tidyLPA

Easily carry out Latent Profile Analysis (LPA) using open-source or commercial software

Last synced: 13 Aug 2026

https://github.com/xoolive/traffic

A toolbox for processing and analysing air traffic data

adsb air-traffic-data data-analytics data-science data-visualisation declarative-pipeline mode-s trajectory

Last synced: 13 Aug 2026

https://github.com/SMTG-Bham/sumo

Heavyweight plotting tools for ab initio calculations

computational-chemistry materials-science plotting python

Last synced: 13 Aug 2026

https://github.com/roualdes/bridgestan

BridgeStan provides efficient in-memory access through Python, Julia, and R to the methods of a Stan model.

c cpp julia python r stan

Last synced: 12 Aug 2026

https://github.com/jrkerns/pylinac

An image analysis library for medical physics

image-analysis image-processing medical-physics python radiation-oncology

Last synced: 12 Aug 2026

https://github.com/ropensci/USAboundaries

Historical and Contemporary Boundaries of the United States of America

digital-history history r r-package rstats spatial-data

Last synced: 13 Aug 2026

https://github.com/materialsproject/pymatgen-analysis-defects

Defect analysis modules for pymatgen

Last synced: 12 Aug 2026

https://github.com/mbhall88/rasusa

Randomly subsample sequencing reads or alignments

alignment bam bioinformatics coverage downsample fasta fastq genome-analysis random rust subsampling

Last synced: 13 Aug 2026

https://github.com/spacetx/starfish

starfish: unified pipelines for image-based transcriptomics

human-cell-atlas imaging python transcriptomics

Last synced: 13 Aug 2026

https://github.com/hainegroup/oceanspy

A Python package to facilitate ocean model data analysis and visualization.

ocean oceanography physical-oceanography

Last synced: 13 Aug 2026

https://github.com/spectrapepper/spectrapepper

A Python package for advanced processing and combinatorial analysis of spectroscopy data.

Last synced: 13 Aug 2026

https://github.com/volkamerlab/opencadd

A Python library for structural cheminformatics

Last synced: 13 Aug 2026

https://github.com/drostlab/philentropy

Information Theory and Distance Quantification with R

distance-measures distance-quantification information-theory jensen-shannon-divergence parametric-distributions r similarity-measures statistics

Last synced: 13 Aug 2026

https://github.com/ReactiveBayes/RxInfer.jl

Julia package for automated Bayesian inference on a factor graph with reactive message passing

bayesian-inference inference-engine julia-language machine-learning message-passing probabilistic-programming variational-inference

Last synced: 13 Aug 2026

https://github.com/chocoteam/choco-solver

An open-source Java library for Constraint Programming

constraint-optimisation-problem constraint-programming constraint-satisfaction-problem constraint-solver constraints copr csp java solver

Last synced: 12 Aug 2026

https://github.com/mpl-extensions/mpl-interactions

Sliders to control matplotlib and other interactive goodies. Works in any interactive backend and even uses ipywidgets when in a Jupyter notebook

ipympl jupyter jupyter-widgets jupyterlab matplotlib python

Last synced: 12 Aug 2026

https://github.com/Toloka/crowd-kit

Control the quality of your labeled data with the Python tools you already know.

aggregations annotation crowd crowdsourcing data-mining data-science labeling python quality-control toloka truth-inference

Last synced: 12 Aug 2026

https://github.com/icb-dcm/pyabc

distributed, likelihood-free inference

abc approximate-bayesian-inference likelihood-free-inference parameter-inference

Last synced: 12 Aug 2026

https://github.com/karllark/dust_extinction

Astronomical Dust Extinction

astronomy astrophysics astropy dust dust-extinction extinction hacktoberfest

Last synced: 13 Aug 2026

https://github.com/perfanalytics/pose2sim

Markerless kinematics with any cameras — From 2D Pose estimation to 3D OpenSim motion

3d-kinematics biomechanics blender kinematics markerless mocap motion-capture openpose opensim pose-estimation sports

Last synced: 13 Aug 2026

https://github.com/Deltares/hydromt

HydroMT: Automated and reproducible model building and analysis

geoscience hydrodynamics hydrology modeling

Last synced: 13 Aug 2026

https://github.com/gavinsimpson/gratia

ggplot-based graphics and useful functions for GAMs fitted using the mgcv package

distributional-regression gam gamm generalized-additive-mixed-models generalized-additive-models ggplot2 glm lm mgcv penalized-spline r r-package random-effects smoothing splines

Last synced: 12 Aug 2026

https://github.com/vmtk/vmtk

the Vascular Modeling Toolkit

Last synced: 13 Aug 2026

https://github.com/handley-lab/anesthetic

Nested Sampling post-processing and plotting

bayesian-inference fastkde matplotlib mcmc nested-sampling numpy pandas samples scipy

Last synced: 13 Aug 2026

https://github.com/GalacticDynamics/unxt

Unitful Quantities in JAX

array auto-differentiation dimensions high-performance jax quantities scientific-computing units

Last synced: 12 Aug 2026

https://github.com/ropensci/nomisr

Access UK official statistics from the Nomis database through R.

api-client census-data demography geographic-data national-statistics official-statistics officialstatistics peer-reviewed r r-package rstats uk

Last synced: 13 Aug 2026

https://github.com/VincentStimper/normalizing-flows

PyTorch implementation of normalizing flow models

density-estimation glow invertible-neural-networks neural-spline-flow normalizing-flow pytorch real-nvp residual-flow variational-autoencoder variational-inference

Last synced: 12 Aug 2026

https://github.com/JacksonBurns/astartes

Better Data Splits for Machine Learning

ai data-science machine-learning ml python sampling

Last synced: 12 Aug 2026

https://github.com/mscroggs/symfem

A symbolic finite element definition library

finite-elements symbolic-algebra

Last synced: 13 Aug 2026

https://github.com/ocean-eddy-cpt/gcm-filters

Diffusion-based Spatial Filtering of Gridded Data

Last synced: 13 Aug 2026

https://github.com/HLasse/TextDescriptives

A Python library for calculating a large variety of metrics from text

dependency-distance descriptive-statistics nlp python readability readability-scores spacy spacy-extension statistics syntactic-analysis

Last synced: 13 Aug 2026

https://github.com/glotzerlab/coxeter

Collection of tools to help initialize and manipulate geometries in two and three dimensions.

computational-geometry geometry physics polygons polyhedra shapes

Last synced: 13 Aug 2026

https://github.com/vnmabus/rdata

A Python library for R datasets.

conversion python python3 r rda rdata rds

Last synced: 12 Aug 2026

https://github.com/Music-and-Culture-Technology-Lab/omnizart

Omniscient Mozart, being able to transcribe everything in the music, including vocal, drum, chord, beat, instruments, and more.

beat-tracking chord drum-transcription music-information-retrieval music-transcription vocal

Last synced: 13 Aug 2026

https://github.com/devsim/devsim

TCAD Semiconductor Device Simulator

c-plus-plus devsim finite-volume pde python semiconductor semiconductor-physics tcad tcad-device-simulator

Last synced: 13 Aug 2026

https://github.com/MillionConcepts/pdr

[P]lanetary [D]ata [R]eader - A single function to read all Planetary Data System (PDS) data into Python

Last synced: 13 Aug 2026

https://github.com/fermisurfaces/IFermi

Fermi surface generation, analysis and visualisation.

fermi-slice fermi-surface vasp

Last synced: 13 Aug 2026

https://github.com/adrn/schwimmbad

A common interface to processing pools.

mpi multiprocessing parallel-computing

Last synced: 13 Aug 2026

https://github.com/neurodsp-tools/neurodsp

Digital signal processing for neural time series.

Last synced: 13 Aug 2026

https://github.com/JuliaDynamics/ResumableFunctions.jl

C# style generators a.k.a. semi-coroutines for Julia.

finite-state-machine iterator julia semi-coroutine stackless

Last synced: 13 Aug 2026

https://github.com/vprusso/toqito

|toqito> (Theory of Quantum Information Toolkit) is a Python library for research in quantum information theory.

convex-optimization entanglement linear-algebra matrix-analysis nonlocal-game physics python python-3 quantum quantum-channels quantum-computing quantum-information quantum-information-science quantum-information-theory quantum-measurements quantum-physics quantum-programming quantum-states research semidefinite-programming

Last synced: 13 Aug 2026

https://github.com/PyAutoLabs/PyAutoLens

PyAutoLens: Open-Source Strong Gravitational Lensing

astronomy astrophysics bayesian-inference cosmology galaxy gravitational-lensing python

Last synced: 13 Aug 2026

https://github.com/ropensci/plater

Tools to make it easy to work with microtiter plate-shaped data

r r-package rstats

Last synced: 13 Aug 2026

https://github.com/N-Wouda/ALNS

Adaptive large neighbourhood search (and more!) in Python.

adaptive-large-neighbourhood-search alns cutting-stock-problem flow-shop metaheuristic operations-research python rcpsp scheduling-problem travelling-salesman-problem tsp vehicle-routing-problem vrp