JOSS collection | Ecosyste.ms: Summary

https://github.com/ghislainv/forestatrisk

📦🐍 Python package to model and forecast the risk of deforestation

biodiversity-scenario co2-emissions deforestation deforestation-risk forecasting forest-cover-change ipbes ipcc land-use-change protected-areas python redd roads spatial-analysis spatial-autocorrelation spatial-modelling tropical-forests

Last synced: 29 Sep 2026

https://github.com/ajakef/gemlog

Data conversion software for the Gem Infrasound Logger

infrasound miniseed

Last synced: 29 Sep 2026

https://github.com/expfactory/expfactory

software to generate a reproducible container with a battery of experiments

battery container experiment-factory experiments expfactory psychology reproducible singularity

Last synced: 29 Sep 2026

https://github.com/undark-lab/swyft

A system for scientific simulation-based inference at scale.

likelihood-free-inference machine-learning marginal-neural-ratio-estimation neural-ratio-estimation parameter-estimation python pytorch simulation-based-inference truncated-neural-ratio-estimation

Last synced: 29 Sep 2026

https://github.com/ThomasMBury/ewstools

Python package for early warning signals (EWS) of critical transitions in time series data.

autocorrelation bifurcation bootstrapping complex-systems critical-transitions early-warning-indicators early-warning-signals forecasting ipynb power-spectrum python resilience-indicators time-series tipping-point visualization

Last synced: 29 Sep 2026

https://github.com/hauselin/ollama-r

R library to run Ollama language models

ai api llm llms ollama ollama-api r

Last synced: 29 Sep 2026

https://github.com/floodlight-sports/floodlight

Python package for streamlined analysis of sports data.

python sports-analytics sports-stats

Last synced: 29 Sep 2026

https://github.com/beniaminogreen/zoomerjoin

Superlatively-fast fuzzy-joins in R

blazinglyfast fuzzyjoin join r r-package rstats rust zoomer

Last synced: 29 Sep 2026

https://github.com/dazhwu/pydynpd

This python package estimates dynamic panel data model using difference GMM and system GMM.

arellano-bond data dynamic dynamic-panel-data panel system-gmm

Last synced: 29 Sep 2026

https://github.com/terrytangyuan/dml

R package for Distance Metric Learning

dimensionality-reduction distance-metric-learning machine-learning metric-learning r statistics

Last synced: 29 Sep 2026

https://github.com/k3jph/phonics-in-r

Phonetic Spelling Algorithms in R

bsd-2-license linguistics metaphone nysiis phonetic-spelling-algorithms phonics record-linkage soundex text-processing

Last synced: 29 Sep 2026

https://github.com/AgrDataSci/climatrends

Climate Variability Indices for Ecological Modelling

climate-data climatology timeseries-analysis

Last synced: 29 Sep 2026

https://github.com/hpgem/nanomesh

Python workflow tool for generating meshes from 2D and 3D image data

finite-element-methods image-processing meshing microscopy python

Last synced: 29 Sep 2026

https://github.com/brainets/frites

Framework for Information Theoretical analysis of Electrophysiological data and Statistics

brainhack brainhack-marseille brainweb cluster-based electrophysiological-data ffx functional-connectivity gaussian-copula group-level information-theory institut-neurosciences-timone neurophysiological-data rfx statistics

Last synced: 29 Sep 2026

https://github.com/OSeMOSYS/otoole

OSeMOSYS Tools for Energy

energy energy-system energy-system-modelling osemosys

Last synced: 29 Sep 2026

https://github.com/jorgensd/adios4dolfinx

Extending DOLFINx with checkpointing functionality

adios2 checkpointing fenicsx mpi-applications

Last synced: 29 Sep 2026

https://github.com/ianfhunter/GNOLL

GNOLL is an efficient dice notation parser for multiple programming languages that supports a wide set of dice notation

board-game c cpp dice dice-notation dice-roller dice-rolls go golang haskell java javascript js julia perl python r roleplaying-games rpg-dice-roller ttrpg

Last synced: 29 Sep 2026

https://github.com/arvestad/alv

A console-based alignment viewer

Last synced: 29 Sep 2026

https://github.com/pyro-kinetics/pyrokinetics

Python library to run and analyse gyrokinetics simulations

Last synced: 29 Sep 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: 29 Sep 2026

https://gitlab.com/cosapp/cosapp

CoSApp core package

Last synced: 29 Sep 2026

https://github.com/GEUS-Glaciology-and-Climate/pypromice

Process AWS data from L0 (raw logger) through Lx (end user)

greenland weather weather-station

Last synced: 29 Sep 2026

https://github.com/simple-crypto/SCALib

Side-Channel Analysis Library

Last synced: 29 Sep 2026

https://github.com/CoLRev-Environment/bib-dedupe

Last synced: 29 Sep 2026

https://github.com/FourierFlows/GeophysicalFlows.jl

Geophysical fluid dynamics pseudospectral solvers with Julia and FourierFlows.jl.

baroclinic fourierflows geophysical-fluid-dynamics gpu julia navier-stokes pdes qg quasigeostrophy sqg

Last synced: 29 Sep 2026

https://github.com/mad-lab-fau/imucal

A Python library to calibrate 6 DOF IMUs

Last synced: 29 Sep 2026

https://github.com/sylvaticus/BetaML.jl

Beta Machine Learning Toolkit

ai artificial-intelligence autoencoder classification clustering data-science decision-trees deep-learning feature-importance imputation julia machine-learning ml neural-networks pca random-forest regression

Last synced: 29 Sep 2026

https://github.com/mviereck/x11docker

Run GUI applications and desktops in docker and podman containers. Focus on security.

containers desktop docker gpu gui html5 nerdctl podman printer pulseaudio sandbox sound ssh vnc wayland webcam x x11 xorg xpra

Last synced: 30 Sep 2026

https://github.com/HeloiseS/hoki

Bridging the gap between observation and theory

Last synced: 29 Sep 2026

https://github.com/NKI-AI/direct

Deep learning framework for MRI reconstruction

deep-learning fastmri-challenge inverse-problems medical-imaging mri-reconstruction pytorch

Last synced: 29 Sep 2026

https://github.com/acerbilab/pybads

PyBADS: Bayesian Adaptive Direct Search optimization algorithm for model fitting in Python

bayesian-optimization log-likelihood noiseless-functions noisy-functions optimization-algorithms python

Last synced: 29 Sep 2026

https://github.com/jamesrhester/Lerche.jl

A Julia port of the Lark parser

Last synced: 29 Sep 2026

https://github.com/seisman/HinetPy

A Python package for accessing and processing NIED Hi-net seismic data.

hinet python sac seismology win32

Last synced: 29 Sep 2026

https://github.com/pyroll-project/pyroll-core

PyRoll rolling simulation framework - core library.

groove-rolling materials metal-forming pyroll python rolling simulation

Last synced: 29 Sep 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: 29 Sep 2026

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

A Julia package for generating timeseries surrogates

hacktoberfest hypothesis-testing julia nonlinear-time-series surrogate surrogates timeseries

Last synced: 29 Sep 2026

https://github.com/CLARIAH/grlc

grlc builds Web APIs using shared SPARQL queries

api linked-data linked-data-api open-api semantic-web sparql swagger-ui

Last synced: 29 Sep 2026

https://github.com/silvandeleemput/memcnn

PyTorch Framework for Developing Memory Efficient Deep Invertible Networks

deep-learning machine-learning python3 pytorch

Last synced: 29 Sep 2026

https://github.com/MagneticParticleImaging/MPIFiles.jl

Julia Package for reading and writing MPI Files

julia mpi

Last synced: 30 Sep 2026

https://github.com/BioPandas/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 29 Sep 2026

https://gitlab.com/fame-framework/fame-io

Python package for input file creation for FAME models and digestion of FAME outputs. [Documentation](https://fame-framework.gitlab.io/fame-io/)

FAME

Last synced: 29 Sep 2026

https://github.com/lucydot/effmass

Calculates various definitions of effective mass from the electronic bandstructure of a semiconductor.

Last synced: 29 Sep 2026

https://github.com/TeaspoonTDA/teaspoon

Topological Signal Processing in Python

persistent-homology persistent-homology-graphs python signal-processing tda tda-python topological-data-analysis topological-signal-processing

Last synced: 29 Sep 2026

https://github.com/jeremiah-corrado/fem_2d

A rust library for 2D Finite Element Method computations

Last synced: 29 Sep 2026

https://github.com/flatironinstitute/neurosift

Browser-based NWB visualization and DANDI exploration

dandi live neurosift nwb pypi

Last synced: 29 Sep 2026

https://github.com/casics/nostril

Nostril: Nonsense String Evaluator

detector gibberish identifier-string identifiers inference mining-software-repositories nonsense nonsense-string-evaluator source-code text-processing

Last synced: 29 Sep 2026

https://github.com/opengeos/lidar

A Python package for delineating nested surface depressions from digital elevation data.

digital-elevation-model gis hydrological image-processing lidar python remote-sensing terrain-analysis

Last synced: 29 Sep 2026

https://github.com/pybamm-team/liionpack

A battery pack simulation tool that uses the PyBaMM framework

Last synced: 29 Sep 2026

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

Functional Posterior Plotter

astrophysics astrostatistics bayesian-inference cosmology matplotlib plotting statistics

Last synced: 29 Sep 2026

https://github.com/ImperialCollegeLondon/PyProBE

Python Processing for Battery Experiments

Last synced: 29 Sep 2026

https://github.com/daijiang/hillR

An R pakage to calculate diversity through Hill Numbers

biodiversity hill-numbers r

Last synced: 29 Sep 2026

https://github.com/ropensci/chirps

API Client for CHIRPS

chirps climatology precipitation-data rstats

Last synced: 29 Sep 2026

https://github.com/eendebakpt/oapackage

Orthogonal Array package

Last synced: 29 Sep 2026

https://github.com/OceanBioME/OceanBioME.jl

🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics

biogeochemical-models biogeochemistry climate julia ocean ocean-modelling ocean-sciences oceanography

Last synced: 29 Sep 2026

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

Band structure unfolding made easy!

ab-initio band-structure-unfolding computational-chemistry computational-materials-science defects dft disorder electronic-structure symmetry-breaking unfolding vasp

Last synced: 29 Sep 2026

https://github.com/SongshGeoLab/ABSESpy

An Agent-based Social-ecological System python framework for coupling human-nature researches.

Last synced: 29 Sep 2026

https://github.com/mnets/pymnet

The original library for analyzing multilayer networks.

multilayer-networks network-analysis python

Last synced: 29 Sep 2026

https://github.com/acerbilab/pyvbmc

PyVBMC: Variational Bayesian Monte Carlo algorithm for posterior and model inference in Python

bayesian-inference data-analysis gaussian-processes machine-learning python variational-inference

Last synced: 29 Sep 2026

https://github.com/hugoledoux/startinpy

A Python library for modelling and processing 2.5D terrains using a (2D) Delaunay triangulation.

delaunay-triangulation gis interpolation terrain tin

Last synced: 29 Sep 2026

https://github.com/aymgal/COOLEST

Standard for strong gravitational lensing analyses

astrophysics gravitational-lensing lens-modeling standardization

Last synced: 29 Sep 2026

https://github.com/masadcv/FastGeodis

Fast Implementation of Generalised Geodesic Distance Transform for CPU (OpenMP) and GPU (CUDA)

deep-learning gpu pytorch

Last synced: 29 Sep 2026

https://github.com/hope-data-science/tidyfst

Tidy Verbs for Fast Data Manipulation

Last synced: 29 Sep 2026

https://github.com/spjuhel/BoARIO

Python implementation of ARIO model

Last synced: 29 Sep 2026

https://github.com/bastistician/polyCub

An R package for numerical integration over polygonal domains

numerical-integration polygons r

Last synced: 29 Sep 2026

https://github.com/SteveMacenski/slam_toolbox

Slam Toolbox for lifelong mapping and localization in potentially massive maps with ROS

Last synced: 29 Sep 2026

https://github.com/SwissClinicalTrialOrganisation/secuTrialR

Handling of data from the clinical data management system secuTrial

Last synced: 29 Sep 2026

https://github.com/delira-dev/delira

Lightweight framework for fast prototyping and training deep neural networks with PyTorch and TensorFlow

deep-learning delira machine-learning medical-images medical-imaging pytorch radiology tensorflow

Last synced: 29 Sep 2026

https://github.com/DeepRank/deeprank2

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

convolutional-neural-networks deep-learning graph-neural-networks protein-protein-interfaces pytorch single-residue-variants structural-biology

Last synced: 29 Sep 2026

https://github.com/mzy2240/ESA

Easy SimAuto (ESA): An easy-to-use Power System Analysis Automation Environment atop PowerWorld Simulator Automation Server (SimAuto)

automation contingency-analysis esa graph-analysis hpc numba numpy pandas power-flow powersystem powerworld powerworld-simulator python pythran simauto simulator simulator-automation-server smart-grid transient-stability

Last synced: 29 Sep 2026

https://github.com/ECSIM/opem

OPEM (Open Source PEM Fuel Cell Simulation Tool)

chemistry dynamic-analysis electrochemistry fuel-cell opem pem physics physics-simulation python script simulation simulator static-analysis static-analyzer

Last synced: 29 Sep 2026

https://github.com/robwschlegel/heatwaveR

This GitHub repo contains all of the code for the heatwaveR package.

Last synced: 29 Sep 2026

https://github.com/UofUEpiBio/epiworldR

A general framework for quick epidemiological ABM models

abm agent-based-modeling covid-19 epidemics epidemiology r-package r-programming rpack rpkg seir seir-model simulation sir sir-model

Last synced: 29 Sep 2026

https://github.com/bihealth/altamisa

AltamISA: a Python API for ISA-Tab files

bioinformatics isa isa-tab

Last synced: 29 Sep 2026

https://github.com/watts-dev/watts

Workflow and Template Toolkit for Simulation (WATTS)

mcnp nuclear-energy openmc python simulation templates workflow-automation

Last synced: 29 Sep 2026

https://github.com/rivasiker/PhaseTypeR

General-purpose phase-type functions

Last synced: 29 Sep 2026

https://github.com/gbouras13/dnaapler

Reorients assembled microbial sequences

Last synced: 29 Sep 2026

https://gitlab.com/mauricemolli/petitRADTRANS

Last synced: 29 Sep 2026

https://github.com/ynop/audiomate

Python library for handling audio datasets.

audio audio-datasets corpus-tools data-loader dataset-creation dataset-filtering dataset-manager music noise speech speech-recognition

Last synced: 29 Sep 2026

https://github.com/DeltaRCM/pyDeltaRCM

Delta model with a reduced-complexity approach

Last synced: 29 Sep 2026

https://github.com/sambit-giri/tools21cm

21-cm-cosmology 21-cm-powerspectrum cosmic-dawn epoch-of-reionization reionization

Last synced: 29 Sep 2026

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

Python tools for spatial trajectory and time-series data analysis

animal-behavior python spatial-data-analysis time-series-analysis trajectory-analysis

Last synced: 29 Sep 2026

https://github.com/eddelbuettel/rcppcnpy

Rcpp bindings for NumPy files

c-plus-plus cran numpy r r-package

Last synced: 29 Sep 2026

https://github.com/bjmorgan/py-sc-fermi

py-sc-fermi is a materials modelling code for calculating self-consistent Fermi energies and defect concentrations under thermodynamic equilibrium (or quasi-equilibrium) given defect formation energies.

Last synced: 29 Sep 2026

https://gitlab.com/libreumg/dataquier

Data quality assessments <https://doi.org/10.21105/joss.03093> guided by a data quality framework <https://doi.org/10.1186/s12874-021-01252-7> target the data quality dimensions integrity, completeness, consistency, and accuracy.

data quality

Last synced: 29 Sep 2026