JOSS collection | Ecosyste.ms: Summary

https://github.com/ttricco/sarracen

A Python library for smoothed particle hydrodynamics (SPH) analysis and visualization.

Last synced: 15 Aug 2026

https://github.com/HeloiseS/hoki

Bridging the gap between observation and theory

Last synced: 15 Aug 2026

https://github.com/pencil-code/pencil-code

A high-order finite-difference code for compressible hydrodynamic flows with magnetic fields and particles

Last synced: 15 Aug 2026

https://github.com/hydroframe/hf_hydrodata

Last synced: 15 Aug 2026

https://github.com/databio/simpleCache

Simplified R caching for reproducible big data projects

Last synced: 15 Aug 2026

https://github.com/powerfulbean/mTRFpy

a python3 version of matlab mTRF-Toolbox by Lalor Lab https://mtrfpy.readthedocs.io/

eeg lalorlab python temporal-response-function

Last synced: 16 Aug 2026

https://github.com/alexlenail/NN-SVG

Publication-ready NN-architecture schematics.

d3 deep-learning diagrams drawing machine-learning neural-network svg threejs

Last synced: 15 Aug 2026

https://github.com/jdidion/xphyle

Python library that facilitates opening, reading, and writing files (and file-like entities like URLs and streams) agnostic of compression format. (production)

Last synced: 15 Aug 2026

https://github.com/ECRL/ecabc

Artificial bee colony optimizer for user-defined parametric fitness functions

artificial-bee-colony feature-tuning hyperparameter-optimization neural-network

Last synced: 15 Aug 2026

https://github.com/statdivlab/rigr

Regression, Inference, and General Data Analysis Tools for R

regression statistics

Last synced: 15 Aug 2026

https://github.com/Alcampopiano/hypothesize

Robust statistics in Python

confidence-intervals data-analysis hypothesis-testing null-hypothesis python r robust-statistics significance-testing statistics stats

Last synced: 15 Aug 2026

https://github.com/PlanetFormationLab/eddy

Python tools to recover precise rotation profiles of disks.

Last synced: 15 Aug 2026

https://github.com/prmiles/pymcmcstat

Python implementation of MATLAB toolbox "mcmcstat"

adaptive-metropolis delayed-rejection markov-chain-monte-carlo mcmc metropolis-hastings python

Last synced: 15 Aug 2026

https://github.com/delve-team/delve

PyTorch model training and layer saturation monitor

convolutional-neural-networks deep-learning layer-saturation model-training neural-dynamics pruning pytorch training-monitor visualization

Last synced: 15 Aug 2026

https://github.com/DLR-AMR/t8code

Parallel algorithms and data structures for tree-based adaptive mesh refinement (AMR) with arbitrary element shapes.

adaptive-mesh-refinement high-performance-computing hpc mesh modeling mpi parallel parallel-computing simulation

Last synced: 15 Aug 2026

https://github.com/SebastianBocquet/pygtc

Make a sweet giant triangle confusogram (GTC) plot

bayesian-data-analysis data-visualization mcmc

Last synced: 15 Aug 2026

https://gitlab.com/vibes-developers/vibes

[FHI-vibes](https://vibes-developers.gitlab.io/vibes/): Vibrational simulations with python powered by ASE and FHI-aims.

Last synced: 15 Aug 2026

https://github.com/CLOVER-energy/CLOVER

CLOVER minigrid simulation and optimisation for supporting rural electrification in developing countries

Last synced: 15 Aug 2026

https://github.com/fellstat/ipc

Tools for message passing between processes

Last synced: 15 Aug 2026

https://github.com/daya6489/SmartEDA

a R package for data exploratory analysis

analysis exploratory-data-analysis

Last synced: 15 Aug 2026

https://github.com/gesistsa/oolong

🍵 Create and administrate validation tests for automated content analysis tools.

r textanalysis topicmodeling validation

Last synced: 15 Aug 2026

https://github.com/mggg/ecological-inference

Ecological inference, in Python

Last synced: 15 Aug 2026

https://github.com/marchirschvogel/ambit

FEniCSx-based cardiovascular multi-physics solver

Last synced: 15 Aug 2026

https://github.com/jeremiecoullon/SGMCMCJax

Lightweight library of stochastic gradient MCMC algorithms written in JAX.

bayesian-inference jax sampling-methods

Last synced: 15 Aug 2026

https://github.com/tdaverse/TDAstats

R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.

cran data-science ggplot2 homology homology-calculations homology-computation joss persistent-homology pipeline r r-package r-packages ripser tda topological-data-analysis topology topology-visualization visualization

Last synced: 15 Aug 2026

https://github.com/passaH2O/dorado

For shallow-water Lagrangian particle routing.

hydrodynamic-modeling lagrangian numerical-modeling numerical-modelling particle particle-routing particle-tracing particle-tracking particle-transport particles passive-tracers random-walk rivers simulator tracer

Last synced: 15 Aug 2026

https://github.com/Yu-Group/veridical-flow

Making it easier to build stable, trustworthy data-science pipelines based on the PCS framework.

ai data-science ensembling machine-learning ml pandas preprocessing python3 stability statistics tutorial workflow

Last synced: 15 Aug 2026

https://github.com/paudetseis/Telewavesim

Teleseismic body wave modeling through stacks of (submarine/anisotropic) layers

anisotropy fortran geophysics modeling obs plane-waves python receiver-functions seismology sks

Last synced: 15 Aug 2026

https://github.com/brainets/hoi

Higher-Order Interactions

higher-order-interactions hoi jax network python

Last synced: 15 Aug 2026

https://github.com/sandialabs/pvOps

A set of documented functions for supporting operations research of photovoltaic energy systems.

scr-2609 snl-data-analysis snl-visualization

Last synced: 16 Aug 2026

https://github.com/ArcticSnow/TopoPyScale

TopoPyScale: a Python library to perform simplistic climate downscaling at the hillslope scale

climate climate-science clustering dem downscaling era5 geoscience joss science timeseries xarray

Last synced: 15 Aug 2026

https://github.com/ECP-copa/Cabana

Performance-portable library for particle-based simulations

co-design exascale exascale-computing high-performance-computing hpc kokkos particles

Last synced: 15 Aug 2026

https://github.com/USEPA/harmonize-wq

Standardize, clean, and wrangle Water Quality Portal data into more analytic-ready formats

ord research

Last synced: 15 Aug 2026

https://github.com/IPESE/REHO

Decision Support Tool for Renewable Energy Communities

Last synced: 15 Aug 2026

https://github.com/dirmeier/datastructures

:rocket: Implementation of core data structures for R

algorithms datastructures r rcpp

Last synced: 15 Aug 2026

https://github.com/r-causal/tipr

An R package for conducting sensitivity analyses for unmeasured confounders

Last synced: 15 Aug 2026

https://github.com/Rhyd-Lewis/GCol

A Python library for graph coloring

Last synced: 16 Aug 2026

https://github.com/krober10nd/SeismicMesh

2D/3D serial and parallel triangular mesh generation tool for finite element methods.

distmesh meshing parallel seismic-velocity-models

Last synced: 15 Aug 2026

https://github.com/gaelforget/MITgcm.jl

Julia interface to MITgcm

adjoint adjoint-sensitivities biogeochemistry climate climate-model climate-science ecology model ocean ocean-modelling ocean-sciences particles seaice tracers transport

Last synced: 15 Aug 2026

https://github.com/nkarasiak/MuseoToolBox

MuseoToolBox : a python library for remote sensing scripts

Last synced: 15 Aug 2026

https://github.com/r-dcm/measr

R package for the Bayesian estimation of diagnostic classification models using Stan

bayesian cdm cmdstanr cognitive-diagnosis cognitive-diagnostic-models dcm diagnostic-classification-models psychometrics r r-package rstan rstats stan

Last synced: 15 Aug 2026

https://github.com/umr-amap/StormR

Funtions to quantify and map the tropical storms and cyclones’ winds characteristics'

cyclones-behaviour r tropical-storms

Last synced: 15 Aug 2026

https://github.com/scikit-tda/DREiMac

Dimensionality Reduction with Eilenberg-MacLane Coordinates

dimensionality-reduction manifold-learning topological-data-analysis

Last synced: 15 Aug 2026

https://github.com/kadyb/rgugik

Download datasets from Polish Head Office of Geodesy and Cartography

cartography geodesy gis open-data poland r

Last synced: 15 Aug 2026

https://github.com/ropensci/daiquiri

Data quality reporting for temporal datasets.

data-quality initial-data-analysis r r-package reproducible-research rstats temporal-data time-series

Last synced: 15 Aug 2026

https://github.com/terminological/dtrackr

An R library for managing and documenting dplyr data pipelines

Last synced: 15 Aug 2026

https://github.com/OttoStruve/muler

A Python package for working with pipeline-produced spectra from IGRINS, HPF, and Keck NIRSPEC

astronomical-algorithms astronomy data-analysis data-science echelle exoplanets infrared python spectroscopy stars stellar-atmospheres

Last synced: 15 Aug 2026

https://github.com/frank1010111/pywaterflood

Capacitance resistance models for waterflood connectivity

petroleum-engineering python reservoir rust

Last synced: 16 Aug 2026

https://github.com/IonRepo/IonDiff

Unsupervised identification and analysis of ion-hopping events in solid state electrolytes.

Last synced: 15 Aug 2026

https://github.com/TommyJones/tidylda

Implements an algorithim for Latent Dirichlet Allocation using style conventions from the [tidyverse](https://style.tidyverse.org/) and [tidymodels](https://tidymodels.github.io/model-implementation-principles/index.html).

Last synced: 15 Aug 2026

https://github.com/bommert/stabm

Stability measures

Last synced: 15 Aug 2026

https://github.com/pyomeca/biorbd

Biomechanical add-ons to the RigidBody Dynamics Library

Last synced: 15 Aug 2026

https://github.com/snek5000/snek5000

:snake: Python framework for Nek5000 :rocket:

cfd closember fluiddyn fluidsim jinja2 nek5000 python simulation snakemake snek5000 workflow

Last synced: 15 Aug 2026

https://github.com/ropensci/restez

:sleeping: :open_file_folder: Create and Query a Local Copy of GenBank in R

dna entrez genbank r r-package rstats sequence

Last synced: 15 Aug 2026

https://github.com/mlr-org/mcboost

Multi-Calibration & Multi-Accuracy Boosting for R

bias-correction bias-detection classification ethics fairness fairness-ai fairness-ml machine-learning post-processing responsible-ai

Last synced: 15 Aug 2026

https://github.com/Open-ET/flux-data-qaqc

Energy Balance Closure Analysis and Eddy Flux Data Post-Processing

Last synced: 15 Aug 2026

https://github.com/ropensci/osmapiR

An R interface to OpenStreetMap API for fetching and saving data from/to the OpenStreetMap database

openstreetmap openstreetmap-api osm osmapi r r-package

Last synced: 15 Aug 2026

https://github.com/mathLab/PINA

Physics-Informed Neural networks for Advanced modeling

Last synced: 15 Aug 2026

https://github.com/actris-cloudnet/mwrpy

Python package for Microwave Radiometer processing in ACTRIS

Last synced: 15 Aug 2026

https://github.com/connectomicslab/connectomemapper3

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

bids bids-apps bidsapp brain chuv connectome dmri docker eeg fmri parcellation pipelines python singularity

Last synced: 15 Aug 2026

https://github.com/NeotomaDB/neotoma2

Repository for the updated neotoma R package.

earthcube neotoma nsf paleoecology r rstats

Last synced: 15 Aug 2026

https://github.com/atmoschem/eixport

Export Emissions to Atmospheric Models

atmospheric-models atmospheric-science emissions exporting-emissions wrf

Last synced: 15 Aug 2026

https://github.com/taxprofiler/taxpasta

TAXnomic Profile Aggregation and STAndardisation

bioinformatics classification metagenomic-classification metagenomics profiling python standardisation taxonomic-classifications taxonomic-profiling

Last synced: 15 Aug 2026

https://github.com/VirtualPlantLab/PlantSimEngine.jl

A framework to build plant models at the scales that matter

crops fspm julia julialang modeling plants simulation

Last synced: 15 Aug 2026

https://github.com/imr-framework/virtual-scanner

An end-to-end hybrid MR simulator/console

mri

Last synced: 15 Aug 2026

https://github.com/jason-neal/eniric

Extended Near InfraRed spectra Information Content analysis.

astronomy doppler python3 radial-velocity spectroscopy

Last synced: 15 Aug 2026

https://github.com/flatironinstitute/neurosift

Browser-based NWB visualization and DANDI exploration

dandi live neurosift nwb pypi

Last synced: 15 Aug 2026

https://github.com/sintefore/TimeStruct.jl

Flexible time structures for optimization modeling

Last synced: 15 Aug 2026

https://github.com/seanpue/graphtransliterator

A graph-based transliteration tool

Last synced: 15 Aug 2026

https://github.com/Cosmoglobe/zodipy

Astropy-affiliated package for zodiacal light simulations. Maintainers: @metinsa, @hermda02, @dncnwtts

astronomy astropy-affiliated infrared-astronomy interplanetary-dust python simulation-physics simulations zodiacal-light

Last synced: 15 Aug 2026

https://github.com/poissonconsulting/checkr

An R package of assertive functions to check the properties of common R objects.

assertion checkr rstats

Last synced: 15 Aug 2026

https://github.com/ekaterinailin/AltaiPony

Find flares in Kepler and TESS light curves. Notebooks for quickstart inside.

Last synced: 15 Aug 2026

https://github.com/patrickfuchs/buildH

:computer: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.

lipids molecular-dynamics-simulation order-parameters python united-atom

Last synced: 15 Aug 2026

https://github.com/Molmed/checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

genomics illumina quality-control sequencing

Last synced: 15 Aug 2026

https://github.com/adrientaudiere/MiscMetabar

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

amplicon amplicon-sequencing biodiversity-informatics ecology illumina metabarcoding ngs-analysis package r r-package visualization

Last synced: 15 Aug 2026

https://github.com/nickelnine37/pykronecker

A python library for creating Kronecker Product operators with efficient lazy computation

Last synced: 15 Aug 2026

https://github.com/RTIInternational/gobbli

Deep learning with text doesn't have to be scary.

deep-learning docker nlp python

Last synced: 15 Aug 2026

https://github.com/matthiasdemuzere/w2w

A python tool that ingests WUDAPT information into WRF.

Last synced: 15 Aug 2026

https://github.com/mendezVKI/MODULO

MODULO (MODal mULtiscale pOd) is a software developed at the von Karman Institute to perform Multiscale Modal Analysis of numerical and experimental data using the mPOD.

Last synced: 15 Aug 2026

https://github.com/bluefoxr/COINr

COINr

Last synced: 15 Aug 2026

https://gitlab.com/mantik-ai/mantik

Python API and CLI for remote submission and monitoring of Python applications on HPC.

high-performance computing python

Last synced: 15 Aug 2026

https://github.com/zizroc/villager

villager is an extensible agent based modeling (ABM) framework for the R language. It supports agents, agent aggregations and their associated resources, as well as flexible data management.

abm agent-based-modeling simulation

Last synced: 15 Aug 2026

https://github.com/weecology/portalr

A collection of functions to summarize the Portal Data

community-ecology ecology small-mammal-trapping

Last synced: 15 Aug 2026

https://github.com/r-spatialecology/shar

:package: Analyse species-habitat associations in R

habitat-association landscape-ecology point-pattern-analysis spatial-analysis

Last synced: 15 Aug 2026

https://github.com/JuliaSmoothOptimizers/DCISolver.jl

Last synced: 15 Aug 2026

https://github.com/WilliamLwj/PyXAB

PyXAB - A Python Library for X-Armed Bandit and Online Blackbox Optimization Algorithms

algorithm automl bandit-algorithms blackbox-optimization continuous-armed-bandit data-science hyperparameter-optimization hyperparameter-tuning lipschitz-bandit machine-learning machine-learning-algorithms online-learning optimization optimization-algorithms reinforcement-learning x-armed-bandit

Last synced: 15 Aug 2026

https://github.com/USCbiostats/partition

A fast and flexible framework for data reduction in R

data-reduction dimensionality-reduction partitional-clustering r

Last synced: 15 Aug 2026

https://github.com/rajeshrinet/pystokes

PyStokes: phoresis and Stokesian hydrodynamics in Python. github.com/rajeshrinet/pystokes

active-colloids active-particles autophoretic-suspensions colloids crystallization cython force-fields hydrodynamic-interactions phase-separation phoretic-interactions pystokes python stokes-flow stokesian-hydrodynamics traction

Last synced: 15 Aug 2026

https://github.com/USCbiostats/slurmR

slurmR: A Lightweight Wrapper for Slurm

bioinformatics hpc rpackage rstats slurm

Last synced: 15 Aug 2026

https://github.com/ph-rast/bmgarch

Bayesian Multivariate GARCH

Last synced: 15 Aug 2026

https://github.com/TomWagg/cogsworth

A Python package for performing self-consistent population synthesis and galactic dynamics simulations

astrophysics galactic-dynamics population-synthesis python

Last synced: 16 Aug 2026

https://github.com/LRydin/KramersMoyal

kramersmoyal: Kramers-Moyal coefficients for stochastic data of any dimension, to any desired order

diffusion drift drift-diffusion kernel-density-estimation nadaraya-watson stochastic stochastic-differential-equations stochastic-process

Last synced: 15 Aug 2026

https://github.com/erling6232/imagedata

Read/write medical image data

Last synced: 15 Aug 2026

https://github.com/markheckmann/OpenRepGrid

An R package for the analysis of repertory grids

repertory-grid repgrid

Last synced: 16 Aug 2026

https://gitlab.com/cerfacs/batman

Statistical analysis for expensive computer codes made easy.

CFD Gaussian process LES ensemble pod polynomial chaos python surrogate model uncertainty quantification uncertainty visualization

Last synced: 15 Aug 2026

https://github.com/mberto79/XCALibre.jl

Julia Finite Volume CFD solver for incompressible and compressible flow. Supports RANS and LES turbulence, unstructured grids in unv and OpenFoam mesh formats.

aerodynamics cfd compressible-aerodynamics compressible-flows computational-fluid-dynamics computational-fluid-simulation gpu-acceleration incompressible-flow julia julia-language julia-package large-eddy-simulation rans