JOSS collection | Ecosyste.ms: Summary

https://github.com/maize-genetics/rTASSEL

R front-end for TASSEL 5

genomic-prediction gwas linkage-disequilibrium

Last synced: 27 Aug 2026

https://github.com/moritzobenauer/ProjectRaccoon

Automated construction of atomistic and coarse-grained models in the PDB format for polymer peptide conjugates.

cheminformatics molecular-dynamics-simulation molecular-modeling pdb-files

Last synced: 27 Aug 2026

https://github.com/uw-comphys/opencmp

OpenCMP is a computational multiphysics software package based on the finite element method. It is primarily intended for physicochemical processes involving significant convective flow.

computational-fluid-dynamics finite-element-methods modeling simulation

Last synced: 27 Aug 2026

https://github.com/difuture-lmu/dsBinVal

ROC-GLM and calibration analysis for DataSHIELD

auc calibration datashield distributed-computing roc

Last synced: 27 Aug 2026

https://github.com/benlansdell/ethome

Tools for machine learning of animal behavior

boris deeplabcut dlc ndx-pose neurodata-without-borders pose-tracking supervised-learning

Last synced: 27 Aug 2026

https://gitlab.com/datafold-dev/datafold/

Python software for identifying dynamical systems and hidden patterns from time series data

Manifold Learning data-driven diffusion maps dynamic mode decomposition dynamical system koopman operator machine learning time series

Last synced: 27 Aug 2026

https://github.com/Sage-Bionetworks/mhealthtools

A modular R package for extracting features from mobile sensor data

Last synced: 27 Aug 2026

https://github.com/PolymerGuy/AXITOM

Axisymmetric recontruction of tomography data acquired by a conical beam

Last synced: 27 Aug 2026

https://github.com/New-Horizons-SPM/scanbot

STM Automation Bot

automation nanonis nanonistcp nc-afm python scanbot spm stm

Last synced: 27 Aug 2026

https://github.com/glottospace/glottospace

Geospatial analysis of linguistic data

Last synced: 27 Aug 2026

https://github.com/Collab4exaNBody/exaDEM

ExaDEM is a HPC software solution in the field of computational simulations. ExaDEM is built on top of exaNBody platform.

dem gpu granular-media hpc mpi

Last synced: 27 Aug 2026

https://github.com/cMadan/ElGateau

ElGateau: A Library for Using the Elgato Stream Deck for Experimental Psychology Research

Last synced: 27 Aug 2026

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

Dealing with slabs for first principles calculations of surfaces

computational-chemistry materials pymatgen python3 science surfaces vasp

Last synced: 27 Aug 2026

https://github.com/mfroeling/QMRITools

Processing and visualization tools for quantitative MRI data

bids denoising diffusion dixon dti extended-phase-graphs fasculation ivim jcoupling muscle nifti noise-suppression registration relaxometry simulation spectroscopy tractography visualization

Last synced: 27 Aug 2026

https://github.com/BlauGroup/RNMC

Last synced: 27 Aug 2026

https://github.com/FEST3D/FEST-3D

The source code for Finite volume Explicit STructured 3Dimensional (FEST-3D) solver.

Last synced: 27 Aug 2026

https://github.com/abel-research/ampscan

ampscan is an open-source Python package for analysis and visualisation of digitised surface scan data, specifically for applications within Prosthetics and Orthotics (P&O), with an aim to improve evidence-based clinical practice towards improved patient outcomes.

3d-models 3d-scanning numpy prosthetics python southampton visualisation vtk

Last synced: 27 Aug 2026

https://github.com/BackmanLab/PWSpy

A Python library dedicated to the analysis of Partial Wave Microscopy (PWS) data.

Last synced: 27 Aug 2026

https://github.com/HybriD3-database/MatD3

Curatable database for experimental and theoretical data on solid materials.

Last synced: 27 Aug 2026

https://github.com/gvegayon/rgexf/

Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others) in R.

gephi gexf gexf-graph-files r rpackage social-network xml

Last synced: 27 Aug 2026

https://github.com/ropensci-archive/Rclean

:warning: ARCHIVED :warning: Isolate essential code to re-produce specific results.

Last synced: 27 Aug 2026

https://github.com/ropensci-archive/hddtools

Hydrological Data Discovery Tools (R package for hydrology and open data)

data60uk grdc hydrology kgclimateclass mopex peer-reviewed precipitation r r-package rstats sepa

Last synced: 27 Aug 2026

https://github.com/muctadir/lama

LaMa, short for Labelling Machine, is an web application developed for aiding in thematic analysis of qualitative data.

angular docker python qualitative-analysis qualitative-research text-labeling thematic-analysis

Last synced: 27 Aug 2026

https://github.com/kegiljarhus/pyBEMT

Implementation of the Blade Element Momentum Theory for turbines and propellers in Python

Last synced: 27 Aug 2026

https://github.com/samplics-org/samplics

Select, weight and analyze complex sample data

estimation officialstatistics sample samplics sampling survey variance weighting

Last synced: 27 Aug 2026

https://github.com/spinicist/riesling

Radial Interstices Enable Speedy Low-Volume Imaging

Last synced: 27 Aug 2026

https://github.com/emptyport/js-emass

This is a JavaScript implementation of the emass algorithm for calculating accurate isotopic envelopes

Last synced: 27 Aug 2026

https://github.com/daniloceano/CycloPhaser

This package calculates extratropical cyclone life cycle phases from vorticity data using Python.

Last synced: 27 Aug 2026

https://github.com/pachadotdev/gravity

R package that provides estimation methods for Gravity Models

bvu bvw ddm econometrics glm gpml gravity international-trade lm maximum-likelihood nbpml nls ols ppml r sils tobit trade

Last synced: 27 Aug 2026

https://github.com/pudu-py/pudu

A Python library for explainability of machine learinng algorithms in an agnostic, deterministic, and simple way.

Last synced: 27 Aug 2026

https://github.com/vergauwenthomas/MetObs_toolkit

A toolkit for using non-traditional meteorological observations

climate meteorology python toolkit

Last synced: 27 Aug 2026

https://github.com/lydialucchesi/Vizumap

R package for visualizing uncertainty in spatial data

Last synced: 27 Aug 2026

https://github.com/Oden-EAG/hp3d

MPI/OpenMP hp-adaptive 3D finite element software

computational-science fem finite-elements high-order hp-adaptivity hpc multiphysics scientific-computing

Last synced: 27 Aug 2026

https://github.com/MartianColonist/POSEIDON

Multidimensional atmospheric retrieval of exoplanet spectra.

Last synced: 27 Aug 2026

https://github.com/zfit/phasespace/

Phase space generation implemented in TensorFlow

hep physics-simulation

Last synced: 27 Aug 2026

https://github.com/grburgess/ronswanson

Ron Swanson builds tables for 3ML

3ml astromodels data-analysis interpolation python ron-swanson spectral-fitting

Last synced: 27 Aug 2026

https://github.com/benjamin-allevius/scanstatistics

An R package for space-time anomaly detection using scan statistics.

anomaly-detection cluster r rcpp rcpparmadillo scan-statistics spatial spatio-temporal statistics

Last synced: 27 Aug 2026

https://github.com/rasg-affiliates/21cmSense

Code for calculating the sensitivity of 21cm experiments to the EoR power spectrum

Last synced: 27 Aug 2026

https://github.com/czbiohub-sf/cerebra

A tool for fast and accurate summarizing of variant calling format (VCF) files

genomics mutations scrna-seq variant-calling

Last synced: 27 Aug 2026

https://github.com/markur4/plotastic

Streamlining statistical analysis by using plotting keywords in Python.

anova data-analysis data-science data-visualization hypothesis-testing matplotlib omnibus pairwise-testing pingouin plotting python seaborn statistical-tests statistics ttest user-friendly

Last synced: 27 Aug 2026

https://github.com/ScottKolo/suitesparse-matrix-collection-website

A web interface for the SuiteSparse Matrix Collection, formerly known as the University of Florida Sparse Matrix Collection

Last synced: 27 Aug 2026

https://github.com/achennu/microbenthos

Modeling framework for microbenthic habitats useful for studies in biogeochemistry and marine microbial ecology.

Last synced: 27 Aug 2026

https://github.com/hcdenbakker/sepia

taxonomic classifier based on the kraken2 algorithms and more

Last synced: 27 Aug 2026

https://github.com/learningsimulator/learningsimulator

Learning Simulator: A simulation software for animal and human learning

associative-learning behavior gui mathematical-modelling python reinforcement-learning simulation

Last synced: 27 Aug 2026

https://github.com/JedS6391/LGP

A robust Linear Genetic Programming implementation on the JVM using Kotlin.

ai genetic-programming gp jvm kotlin lgp linear-genetic-programming machine-learning

Last synced: 27 Aug 2026

https://github.com/mathopt/DynamicOED.jl

Optimal experimental design of ODE and DAE systems in julia

mixed-integer-programming optimal-control optimal-experimental-design sciml

Last synced: 27 Aug 2026

https://github.com/bancaditalia/black-it/

Black-box abm calibration kit by the Bank of Italy

agent-based agent-based-modeling agent-based-simulation calibration-toolbox optimization

Last synced: 27 Aug 2026

https://github.com/Geodels/gospl/

Global Scalable Paleo Landscape Evolution Model

basin-modeling compaction erosion-process landscape landscape-evolution-model lithology paleoclimate paleogeography sediment-transport sedimentation

Last synced: 27 Aug 2026

https://github.com/flyaflya/causact/

causact: R package to accelerate computational Bayesian inference workflows in R through interactive visualization of models and their output.

bayesian-inference dags posterior-probability probabilistic-graphical-models probabilistic-programming rstats-package

Last synced: 27 Aug 2026

https://github.com/bjmt/universalmotif

Motif manipulation functions for R.

motif-analysis motif-enrichment-analysis r sequence-logo

Last synced: 27 Aug 2026

https://github.com/hknd23/idcempy

Inflated Discrete Choice Models

discrete-choice mixture-model multinomial-logistic-regression ordered-probit-regression

Last synced: 27 Aug 2026

https://github.com/FaaSr/FaaSr-package-v1

Function-as-a-Service package for R

Last synced: 27 Aug 2026

https://github.com/mgckind/easyaccess

SQL command line interpreter for astronomical surveys

astronomy interpreter python sql-query

Last synced: 27 Aug 2026

https://github.com/bricoletc/delfies

Querying genomes for evidence of Programmed DNA Elimination

Last synced: 27 Aug 2026

https://github.com/pmcharrison/psychTestR

psychTestR - an R package for developing behavioural experiments

Last synced: 27 Aug 2026

https://github.com/goualard-f/MicroFloatingPoints.jl

A Julia package to manipulate very small IEEE 754 standard-compliant floating-point numbers.

floating-point ieee-754

Last synced: 27 Aug 2026

https://github.com/dshawul/NebulaSEM

Finite Volume (FV) and high-order Discontinuous Galerkin (DG) solver

Last synced: 27 Aug 2026

https://github.com/babinyurii/recan

genetic distance plotting for recombination events analysis

alignment bioinformatics distance-plots dna-recombination genetic-distances python recombination-events virology

Last synced: 27 Aug 2026

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

📡 Open-source physical optics simulation package.

Last synced: 27 Aug 2026

https://github.com/nokaut/wsknn

Session-weighted recommendation system in Python

e-commerce knn machine-learning recommendation-engine recommender-system vsknn

Last synced: 27 Aug 2026

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

Gaussian and Lorentzian smearing of simulated spectra

Last synced: 27 Aug 2026

https://github.com/TriPed-Robot/trip_kinematics

Python package for inverse kinematic calculations of hybrid serial parallel robots

closed-chain hybrid-chain inverse-kinematics kinematic-modeling kinematics manipulator parallel-robot python robotics serial-robotics trajectory-planning

Last synced: 27 Aug 2026

https://github.com/vidarsko/ComFiT

A python library for simulating field theories with topological defects

Last synced: 27 Aug 2026

https://github.com/ronshnapp/MyPTV

MyPTV is an open source library designed for 3D particle Tracking (3D-PTV) measurements

3d-ptv experiments fluid-mechanics measurements particle-tracking photogrammetry python turbulence

Last synced: 27 Aug 2026

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

Create EnergyPlus ready EPW files from observed data.

Last synced: 27 Aug 2026

https://github.com/thermohub/thermofun

A code for calculating the standard state thermodynamic properties at a given temperature and pressure.

chemical-reactions enthalpy entropy equation-of-state geochemical-data geochemical-modeling geochemistry gibbs-energy heat-capacity reaction substance thermodynamic-properties thermodynamics thermodynamics-models

Last synced: 27 Aug 2026

https://github.com/parallelwindfarms/byteparsing

Parser for mixed binary/ASCII data in Python

Last synced: 27 Aug 2026

https://github.com/linuxscout/tashaphyne/

Tashaphyne: Arabic Light Stemmer

Last synced: 27 Aug 2026

https://github.com/devnums/pyheartlib

A Python package for processing electrocardiogram signals ❤️

ecg electrocardiogram machine-learning

Last synced: 27 Aug 2026

https://github.com/lexedata/lexedata

Lexical Data Editing tools

cldf cognates2nexus comparative-linguistics dataset-interface lexicon phylogenetics wordlist

Last synced: 27 Aug 2026

https://github.com/neutrons/multiphonon

multiphonon (getDOS)

Last synced: 27 Aug 2026

https://github.com/nathanael-fijalkow/DeepSynth

DeepSynth is a general-purpose program synthesizer in the programming by example framework: the user provides a few examples as pairs of input and output, DeepSynth finds a program matching the examples.

Last synced: 27 Aug 2026

https://github.com/david-barnett/microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

microbiome microbiome-analysis microbiota r rstats

Last synced: 27 Aug 2026

https://github.com/profjsb/deepCR

Deep Learning Based Cosmic Ray Removal for Astronomical Images

astronomical-images astronomy convolutional-neural-networks deep-learning python3 pytorch

Last synced: 27 Aug 2026

https://github.com/thejasvibr/bat_beamshapes

Directivity functions for various sound sources

acoustics beamshape bioacoustics directivity sound

Last synced: 27 Aug 2026

https://github.com/tlverse/origami

:game_die: :crystal_ball: Comprehensive Cross-Validation Engine

cross-validation machine-learning

Last synced: 27 Aug 2026

https://github.com/chmarti1/PYroMat

PYroMat thermodynamic properties in Python

python thermodynamic-properties thermodynamics

Last synced: 27 Aug 2026

https://github.com/n3mo/massmine

Your Access To Data

Last synced: 27 Aug 2026

https://github.com/everval/LongMemory.jl

Julia package to generate, estimate, and forecast long memory processes

arfima cross-sectional-aggregation forecasting fractional-differencing har-model long-memory long-range-dependence stochastic-duration-shock strong-persistence time-series time-series-analysis

Last synced: 27 Aug 2026

https://github.com/mrilikecoding/StreamPoseML

pose estimation / ML model wrapper and annotation utility

Last synced: 27 Aug 2026

https://github.com/tbrown122387/pf

PF: a header only template library for fast particle filtering!

particle-filter statistical-methods statistical-models statistics

Last synced: 27 Aug 2026

https://github.com/bmorris3/arcesetc

Exposure time calculator for the ARC Echelle Spectrograph (ARCES) on the Apache Point Observatory 3.5 m Telescope

astronomy exposure-calculator spectroscopy

Last synced: 27 Aug 2026

https://github.com/ropensci-archive/jstor

:warning: ARCHIVED :warning: Import journal data from DfR (JSTOR)

jstor peer-reviewed r r-package rstats text-analysis text-mining

Last synced: 27 Aug 2026

https://github.com/tqsd/photon_weave

Photon Weave

jax optics quantum quantum-computing quantum-optics quantum-optics-simulation quantum-physics quantum-simulator

Last synced: 27 Aug 2026

https://github.com/pachadotdev/economiccomplexity

A wrapper of different indices and networks commonly used in Economic Complexity

economic-complexity eigenvalues eigenvectors graphs international-trade matrix networks r recursive-algorithm

Last synced: 27 Aug 2026

https://github.com/KOALA-LMU/coalitions

Coalition probabilities in multi-party democracies

coalition-probabilities election-analysis elections r rstats

Last synced: 27 Aug 2026

https://github.com/EdgeVPNio/evio

Virtualized overlay networking for the fog. The Evio network spans the continuum, from the cloud to the edge, providing a virtual private layer 2 network suitable for edge devices in IoT workloads.

Last synced: 27 Aug 2026