JOSS collection | Ecosyste.ms: Summary

https://github.com/BritishGeologicalSurvey/pyvolcans

Python tool to identify analogue volcanoes via VOLCANS (https://doi.org/10.1007/s00445-019-1336-3)

Last synced: 20 Aug 2026

https://github.com/CEA-MetroCarac/fitspy

Generic tool dedicated to fit spectra in python

decomposition fitting gaussian lmfit lorentzian map python spectral-analysis spectrum

Last synced: 20 Aug 2026

https://github.com/tvwenger/bayes_spec

A Bayesian Spectral Line Modeling Framework

Last synced: 20 Aug 2026

https://github.com/RWTH-EBC/AixCaliBuHA

Wield this tool to be King Arthur of your models.

maintained tool

Last synced: 20 Aug 2026

https://github.com/MAnalytics/opitools

An R-package for opinion analysis of social media data

Last synced: 20 Aug 2026

https://github.com/raamana/graynet

Subject-wise networks from structural MRI, both vertex- and voxel-wise features (thickness, GM density, curvature, gyrification)

anatomical-mri cortical-network cortical-thickness feature-extraction freesurfer graph gray-matter machine-learning mindboggle network-analysis neuroimaging neuroscience structural-mri thickness vbm voxel-based

Last synced: 20 Aug 2026

https://github.com/KarrLab/de_sim

Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling

computational-modelling data-driven-model discrete-event-simulation object-oriented-programming python simulation

Last synced: 20 Aug 2026

https://github.com/hyosubkim/bayes-toolbox

bayes-toolbox

bayesian-inference bayesian-statistics kruschke probabilistic-programming python statistics

Last synced: 21 Aug 2026

https://github.com/cmendl/pytenet

Python implementation of quantum tensor network operations and simulations: matrix product states and operators, TDVP time evolution, support for quantum numbers, ...

Last synced: 20 Aug 2026

https://github.com/parafields/parafields

Parallel Parameter Field Generator for Python

hacktoberfest iwr-hacktoberfest

Last synced: 20 Aug 2026

https://github.com/MichaelSel/edoJS

A set of functions for manipulating musical pitches within a given EDO

Last synced: 20 Aug 2026

https://github.com/virgesmith/humanleague

Microsynthesis using quasirandom sampling and/or IPF

c-plus-plus-11 microsynthesis nodejs python3 quasirandom r sampling-methods

Last synced: 20 Aug 2026

https://github.com/tresoldi/dafsa

Library for computing Deterministic Acyclic Finite State Automata (DAFSA)

Last synced: 20 Aug 2026

https://github.com/akikuno/cstag

Python module to manipulate and visualize minimap2's cs tag

bioinformatics cstag minimap2 python sam sequence

Last synced: 21 Aug 2026

https://github.com/mdolab/pygeo

pyGeo provides geometric design variables and constraints suitable for gradient-based optimization.

mach

Last synced: 20 Aug 2026

https://github.com/IbrahimTanyalcin/lexicon-mono-seq

DOM Text Based Multiple Sequence Alignment Library

alignment animation-library ascii ascii-art async-programming bioinformatics biology data-visualization good-first-issue help-wanted javascript javascript-library msa msa-viewer sequence-alignment vanilla-javascript

Last synced: 20 Aug 2026

https://github.com/complexvariables/ComplexRegions.jl

(Julia) Package for working with curves and regions in the extended complex plane.

Last synced: 20 Aug 2026

https://github.com/PLN-team/pyPLNmodels

Blazing fast inference of PLN models built on top of Python and PyTorch

Last synced: 21 Aug 2026

https://github.com/python-windrose/windrose/

A Python Matplotlib, Numpy library to manage wind data, draw windrose (also known as a polar rose plot), draw probability density function and fit Weibull distribution

matplotlib numpy pandas python speed wind windrose

Last synced: 20 Aug 2026

https://github.com/xianggebenben/GraphSL

Graph Source Localization Library

inverse-problems source-localization

Last synced: 20 Aug 2026

https://github.com/WSWUP/gridwxcomp

Comparison of weather station and gridded climate datasets

bias-correction climate data gridded spatial-analysis weather

Last synced: 21 Aug 2026

https://github.com/evan-l-munson/SAoTD

Sentiment Analysis of Twitter Data (saotd)

bing-lexicon latent-dirichlet-allocation n-grams plot r sentiment-analysis tidy-data topicanalysis tweets twitter-data

Last synced: 20 Aug 2026

https://github.com/athulpg007/AMAT

Home of the Aerocapture Mission Analysis Tool (AMAT). For project documentation visit:

Last synced: 20 Aug 2026

https://github.com/JuliaAI/Imbalance.jl

A Julia toolbox with resampling methods to correct for class imbalance.

class-imbalance classification machine-learning

Last synced: 21 Aug 2026

https://github.com/tleonardi/bedparse

Python module and CLI tool to perform operations on BED files

bed-files bioinformatics cli

Last synced: 20 Aug 2026

https://github.com/project-gemmi/gemmi/

macromolecular crystallography library and utilities

ccp4 cif crystallography mmcif molecular-structures mtz pdb-files protein-structure structural-biology

Last synced: 20 Aug 2026

https://github.com/simoninireland/epyc

Python computational experiment management

Last synced: 20 Aug 2026

https://github.com/IMMM-SFA/tell

A model to predict Total ELectricity Loads (TELL)

Last synced: 20 Aug 2026

https://github.com/glm-tools/pyglmnet/

Python implementation of elastic-net regularized generalized linear models

data-science elastic-net glm lasso machine-learning python

Last synced: 20 Aug 2026

https://github.com/vsoch/citelang

markdown syntax and credit system for software!

citation credit doi publication research-software-engineering rseng

Last synced: 20 Aug 2026

https://github.com/clreda/NORDic

Network-Oriented Repurposing of Drugs Python Package

bandit-algorithm boolean-network drug-repurposing drug-simulation gene-regulatory-network gene-regulatory-network-inference

Last synced: 20 Aug 2026

https://github.com/CLINDA-AAU/ccostr

An R package, ccostr, which calculates estimates of mean cost given censored data

Last synced: 20 Aug 2026

https://github.com/RangamaniLabUCSD/smart

Spatial Modeling Algorithms for Reactions and Transport

Last synced: 21 Aug 2026

https://github.com/ropensci/unifir

A unifying interface for calling Unity from R

cran cran-r r rstats unifir unity unity3d visualization

Last synced: 20 Aug 2026

https://github.com/paulcon/active_subspaces

Python Active-subspaces Utility Library

Last synced: 20 Aug 2026

https://github.com/radicamc/exoTEDRF

Tools for end-to-end reduction of JWST exoplanet observations

atmosphere exoplanet jwst miri niriss nirspec soss spectroscopy teddorf

Last synced: 20 Aug 2026

https://github.com/EcoJulia/Microbiome.jl

For analysis of microbiome and microbial community data

biology ecology julia-language microbiome

Last synced: 20 Aug 2026

https://github.com/noraeisner/LATTE

Lightcurve Analysis Tool for Transiting Exoplanet

Last synced: 20 Aug 2026

https://github.com/mdhaber/scipy/

Scipy library main repository

Last synced: 20 Aug 2026

https://github.com/mdhaber/scipy

Scipy library main repository

Last synced: 20 Aug 2026

https://github.com/JoshKarpel/idesolver

A general-purpose numerical integro-differential equation solver

integro-differential-equations mathematics numerical-integration python

Last synced: 20 Aug 2026

https://github.com/eclipse-archived/golo-lang

Golo - a lightweight dynamic language for the JVM.

golo invokedynamic java jvm language programming-language

Last synced: 20 Aug 2026

https://github.com/limengbinggz/ddtlcm

Last synced: 20 Aug 2026

https://github.com/LuisScoccola/persistable

density-based clustering for exploratory data analysis based on multi-parameter persistence

cluster-analysis clustering clustering-algorithm machine-learning machine-learning-algorithms topological-data-analysis unsupervised-learning

Last synced: 20 Aug 2026

https://github.com/desResLab/LINFA

A Python library for variational inference with normalizing flow and annealing

annealing computational-expensive-models normalizing-flows variational-inference

Last synced: 21 Aug 2026

https://github.com/ktmeaton/NCBImeta

Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).

Last synced: 20 Aug 2026

https://github.com/JuliaOcean/PlanktonIndividuals.jl

This package simulates the behaviors of an ensemble of phytoplankton individuals.

Last synced: 20 Aug 2026

https://github.com/egonw/bacting

Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.

bioclipse bioinformatics blueobelisk cheminformatics excel hacktoberfest rdf

Last synced: 20 Aug 2026

https://github.com/ForsbergPsychometrics/D3mirt

Descriptive 3D Item Response Theory Methods

Last synced: 20 Aug 2026

https://github.com/SCIInstitute/UncertainSCI

Last synced: 21 Aug 2026

https://github.com/GrainLearning/grainLearning

A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials, developed by various projects of the University of Twente (NL), the Netherlands eScience Center (NL), University of Newcastle (AU), and Hiroshima University (JP).

bayesian-inference low-discrepancy-sequences mixture-models parameter-identification sequential-monte-carlo uncertainty-quantification

Last synced: 20 Aug 2026

https://github.com/misken/hillmaker

Occupancy analysis by time of day and day of week, with Python

Last synced: 21 Aug 2026

https://github.com/zoometh/iconr

Formal methods to study Prehistory iconography

archaeology gmm graph-theory iconography network-analysis prehistoric-archaeology rpackage rproject shape-analysis

Last synced: 20 Aug 2026

https://github.com/sidiwang/snSMART

small n sequential multiple assignment randomized trial (snSMART)

bayesian-analysis clinical-trials r rare-disease small-sample

Last synced: 20 Aug 2026

https://github.com/pulseq/pypulseq

Pulseq in Python

mri mri-sequences pulse-sequences pulseq python

Last synced: 20 Aug 2026

https://github.com/ciclope-microFE/ciclope

Computed Tomography to Finite Elements

biomechanics computed-tomography engineering finite-elements python simulation

Last synced: 20 Aug 2026

https://github.com/danilofreire/prisonbrief

An R package that returns tidy data from the World Prison Brief website.

data prison rstats world-prison-brief

Last synced: 20 Aug 2026

https://github.com/nlgranger/SeqTools

A python library to manipulate and transform indexable data (lists, arrays, ...)

delayedcall lazy-evaluation library machine-learning mapping on-the-fly pipeline preprocessing python

Last synced: 20 Aug 2026

https://github.com/Simulation-Decomposition/simdec-python

Sensitivity analysis using simulation decomposition

computational-modeling sensitivity-analysis uncertainty visualization

Last synced: 21 Aug 2026

https://github.com/ropensci/mcbette

Model Comparison using babette

Last synced: 20 Aug 2026

https://github.com/afeinstein20/stella

For characterizing flares with convolutional neural networks

Last synced: 20 Aug 2026

https://gitlab.com/tue-umphy/software/parmesan

**P**ython **A**tmospheric **R**esearch package for **ME**teorological Time**S**eries and Turbulence **AN**alysis

analysis data gas meteorology python

Last synced: 21 Aug 2026

https://github.com/nhejazi/txshift

:package: R/txshift: Efficient Estimation of the Causal Effects of Stochastic Interventions, with Corrections for Outcome-Dependent Sampling

causal-effects causal-inference censored-data machine-learning robust-statistics statistics stochastic-interventions stochastic-treatment-regimes targeted-learning treatment-effects variable-importance

Last synced: 20 Aug 2026

https://github.com/NSAPH-Software/GPCERF

Last synced: 20 Aug 2026

https://github.com/alejandrojuria/tightbinder

General purpose Slater-Koster tight-binding library for electronic structure calculations

alloys band-structure condensed-matter-physics dft-fit disorder electronic-structure physics python simulation slater-koster solid-state-physics tight-binding topology

Last synced: 21 Aug 2026

https://gitlab.com/permafrostnet/teaspoon

Python for permafrost temperature data

dataset earth science geography

Last synced: 21 Aug 2026

https://github.com/mrsonandrade/pyswarming

A research toolkit for Swarm Robotics.

bioinspired engineering math mathematics multi-robot-systems pypi python python-toolkit research robot robotics self-organizing swarm swarm-intelligence swarm-robotics

Last synced: 20 Aug 2026

https://github.com/SESMG/SESMG

Model generator for the optimization of energy systems, based on the modeling framework oemof. No programming skills are required to use it, as the parameters are entered using spreadsheets (e.g. Excel, LibreOffice).

Last synced: 20 Aug 2026

https://github.com/sebhaan/geobo

Python package for Multi-Objective Bayesian Optimisation and Joint Inversion

Last synced: 20 Aug 2026

https://github.com/MayaWaves/mayawaves

Last synced: 21 Aug 2026

https://github.com/pedersen-fisheries-lab/sspm

GAM-based Spatial Surplus Production Models

gam model r spatial surplus

Last synced: 21 Aug 2026

https://github.com/devosoft/Empirical/

A library of tools for scientific software development, with emphasis on also being able to build web interfaces using Emscripten.

Last synced: 20 Aug 2026

https://github.com/paulbrodersen/netgraph/

Publication-quality network visualisations in python

graph graph-tool igraph matplotlib network network-analysis network-science networkx publication-quality-plots python visualization

Last synced: 21 Aug 2026

https://github.com/Brauckhoff/biopixR

R Package for bioimage analysis

Last synced: 21 Aug 2026

https://github.com/ihrke/pypillometry

Pupillometry and eyetracking with python

data data-analysis eye-tracking eyetracking pupillometry

Last synced: 20 Aug 2026

https://github.com/mindearth/mobilkit

A Python Toolkit for Urban Resilience and Disaster Risk Management Analytics using High Frequency Human Mobility Data

Last synced: 21 Aug 2026

https://github.com/Dih5/xpecgen

A python package with a GUI to calculate X-ray sPECtra GENerated in tungsten anodes.

Last synced: 20 Aug 2026

https://github.com/TerrainBento/umami

Calculate topographic metrics for assessing model-data fit

Last synced: 20 Aug 2026

https://github.com/erf-model/ERF

Energy Research and Forecasting Model

amrex atmospheric-modelling

Last synced: 20 Aug 2026

https://github.com/HKUST-OCTAD-LAB/AirTrafficSim

Web-based air traffic simulation and visualization platform for ATM research. Development branch: https://github.com/HKUST-OCTAD-LAB/AirTrafficSim/tree/dev

air-transport atm aviation simulation utm

Last synced: 20 Aug 2026

https://github.com/iagolemos1/thresholdmodeling

Last synced: 20 Aug 2026

https://github.com/LMBooth/pybci

Create real-time BCI's with the LSL, PyTorch, SKLearn and TensorFlow packages.

bci brain-computer-interface hmi human-computer-interaction human-machine-interface labstreaminglayer lsl machine-learning python python-brain-computer-interface pytorch sklearn tensorflow

Last synced: 20 Aug 2026

https://github.com/dgerosa/filltex

Automatic queries to ADS and INSPIRE databases to fill LaTex bibliography

Last synced: 20 Aug 2026

https://github.com/CouncilDataProject/speakerbox

Speakerbox: Fine-tune Audio Transformers for speaker identification.

audio-classification speaker-id speaker-identification transformers

Last synced: 20 Aug 2026

https://github.com/aneeshnaik/lintsampler

Efficient random sampling via linear interpolation.

low-discrepancy-sequence numpy python random-generation random-sampling statistics

Last synced: 20 Aug 2026

https://github.com/UCD4IDS/WaveletsExt.jl

A Julia extension package to Wavelets.jl

ac-wavelets filter julia signal-processing stationary-wavelets wavelet wavelet-transform

Last synced: 20 Aug 2026

https://github.com/pyReef-model/RADWave

A Python interface to perform wave analysis from satellite altimeter data

Last synced: 20 Aug 2026

https://github.com/rahil-makadia/grss

Gauss-Radau Small-body Simulator

asteroids astronomy comets orbit-determination orbit-propagation

Last synced: 21 Aug 2026

https://github.com/mortonne/psifr

Psifr: Analysis and visualization of free recall data

episodic-memory psychology python visualization

Last synced: 20 Aug 2026

https://github.com/tylertrimble/viswaternet

A Python package for easy generation and customization of water distribution network visualizations.

Last synced: 20 Aug 2026

https://github.com/tberlok/paicos

An object-oriented Python package for analysis of (cosmological) simulations performed with Arepo

Last synced: 21 Aug 2026

https://github.com/spiketools/spiketools

Tools for analyzing spiking data from single-neuron recodings.

data-analysis neuroscience python single-unit spike-analysis spikes

Last synced: 20 Aug 2026

https://github.com/NatLabRockies/OpenOA

This library provides a framework for assessing wind plant performance using operational assessment (OA) methodologies that consume time series data from wind plants. The goal of the project is to provide an open source implementation of common data structures, analysis methods, and utility functions relevant to wind plant OA.

Last synced: 20 Aug 2026

https://github.com/Qile0317/APackOfTheClones

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

clonal-analysis immune-repertoire immune-system r scrna-seq scrnaseq seurat single-cell single-cell-genomics

Last synced: 21 Aug 2026