Collections: JOSS
https://github.com/BiomedSciAI/fuse-med-ml
A python framework accelerating ML based discovery in the medical field by encouraging code reuse. Batteries included :)
ai cmmd collaboration ct deep-learning fuse fuse-med-ml fusemedml hacktoberfest healthcare isic knight-challenge machine-learning medical medical-imaging multimodality python pytorch stoic vision
Last synced: 29 Sep 2026
https://github.com/JuliaHEP/UnROOT.jl
Native Julia I/O package to work with CERN ROOT files objects (TTree and RNTuple)
cern-root hacktober hep high-energy-physics julia particle-physics
Last synced: 29 Sep 2026
https://github.com/brocklab/pycashier
cash in on DNA barcode tags
bioinformatics pipeline
Last synced: 29 Sep 2026
https://github.com/pmlmodelling/nctoolkit
A Python package for netCDF analysis and post-processing
cdo netcdf python
Last synced: 29 Sep 2026
https://github.com/underworldcode/underworld2
underworld2: A parallel, particle-in-cell, finite element code for Geodynamics.
auscope docker finite-element-methods geodynamics hacktoberfest hacktoberfest2020 hacktoberfest2021 particle-in-cell petsc python underworld
Last synced: 29 Sep 2026
https://github.com/ahudde/greeks
Sensitivities of Prices of Financial Options and Implied Volatilites
asian-option greeks implied-volatility option r-package
Last synced: 29 Sep 2026
https://github.com/SNEWS2/snewpy
A Python package for working with supernova neutrinos
Last synced: 29 Sep 2026
https://github.com/florisvb/PyNumDiff
Methods for numerical differentiation of noisy data in python
Last synced: 29 Sep 2026
https://github.com/powerapi-ng/powerapi
PowerAPI is a Python framework for building software-defined power meters.
energy energy-monitoring green-computing inria power-meter python
Last synced: 29 Sep 2026
https://github.com/tlverse/hal9001
🤠 📿 The Highly Adaptive Lasso
cross-validation lasso-regression machine-learning-algorithms nonparametric-regression
Last synced: 29 Sep 2026
https://github.com/EdyVision/pii-codex
A research python package for detecting, categorizing, and assessing the severity of personal identifiable information (PII)
analysis data-analysis personal-identifiable-information pii pii-detection poetry presidio python python3 research research-software research-tool
Last synced: 29 Sep 2026
https://github.com/bcgov/ssdtools
An R package to fit and plot Species Sensitivity Distributions (SSDs)
ecotoxicology env rstats species-sensitivity-distribution
Last synced: 29 Sep 2026
https://github.com/edwardoughton/itmlogic
Longley-Rice Irregular Terrain Model (itmlogic)
Last synced: 29 Sep 2026
https://github.com/MintonGroup/swiftest
Swiftest is a software packaged designed to model the long-term dynamical dynamics of n-body systems with a dominant central body, like the solar system.
Last synced: 29 Sep 2026
https://github.com/mmore500/hstrat
hstrat enables phylogenetic inference on distributed digital evolution populations
Last synced: 29 Sep 2026
https://github.com/mattpitkin/psrqpy
A python module to query the ATNF pulsar catalogue
atnf catalogue pulsar python
Last synced: 29 Sep 2026
https://github.com/ropensci/lightr
Import spectral data and related metadata in R
file-import r r-package reproducibility reproducible-research reproducible-science spectral-data spectroscopy
Last synced: 29 Sep 2026
https://github.com/isce-framework/dolphin
InSAR phase linking library for creating surface displacement maps using persistent scatterer (PS) and distributed scatterer (DS) processing
deformation geoscience geospatial-processing insar phase-linking remote-sensing squeesar time-series
Last synced: 29 Sep 2026
https://github.com/NIFTy-PPL/JAXbind
Bind any function written in another language to JAX with support for JVP/VJP/batching/jit compilation
Last synced: 29 Sep 2026
https://github.com/FAU-LAP/NOMAD-CAMELS
We are developing a configurable measurement software (CAMELS), targeted towards the requirements of experimental solid-state physics. Here many experiments utilize a multitude of measurement devices used in dynamically changing setups.
Last synced: 29 Sep 2026
https://github.com/ropensci/UCSCXenaTools
:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
api-client bioinformatics ccle downloader icgc r tcga toil treehouse ucsc ucsc-xena
Last synced: 29 Sep 2026
https://github.com/ornlneutronimaging/braggedgemodeling
Model and analyze neutron Bragg-edge imaging spectra
bragg-edge neutron
Last synced: 29 Sep 2026
https://github.com/python-hydro/pyro2
A framework for hydrodynamics explorations and prototyping
advection astrophysical-simulation finite-volume finite-volume-methods hydrodynamics multigrid pde pyro python simulation solver
Last synced: 29 Sep 2026
https://github.com/EducationalTestingService/rsmtool
A Python package to facilitate research on building and evaluating automated scoring models.
automated-scoring-engines fairness hacktoberfest python scikit-learn scoring-models visualization
Last synced: 29 Sep 2026
https://github.com/ModelOriented/modelStudio
📍 Interactive Studio for Explanatory Model Analysis
ai explainable explainable-ai explainable-machine-learning explanatory-model-analysis human iml interactive interactivity interpretability interpretable interpretable-machine-learning learning machine model model-visualization r visualization xai
Last synced: 29 Sep 2026
https://github.com/Hoosier-Clusters/clusim
An extended package for clustering similarity
Last synced: 29 Sep 2026
https://gitlab.com/materials-modeling/calorine
[A python tool box for GPUMD simulations](https://calorine.materialsmodeling.org/)
atomic scale simulation condensed matter physics force constants gpumd hiphive machine learning potentials molecular dynamics neural network potentials phonons physics python thermal conductivity thermal transport
Last synced: 29 Sep 2026
https://github.com/neuropsychology/psycho.R
An R package for experimental psychologists
apa apa6 bayesian correlation format interpretation mixed-models neuroscience psycho psychology r rstanarm statistics
Last synced: 29 Sep 2026
https://github.com/google/caliban
Research workflows made easy, locally and in the Cloud.
ai-platform docker google-cloud python3 research-tool
Last synced: 29 Sep 2026
https://github.com/tum-pbs/PhiML
Intuitive scientific computing with dimension types for Jax, PyTorch, TensorFlow & NumPy
Last synced: 29 Sep 2026
https://github.com/engnadeau/pybotics
The Python Toolbox for Robotics
calibration doi dynamics hacktoberfest impedance-control inverse-kinematics kinematics math mathematics numpy pypi python python-toolbox research robot robotics scipy trajectory
Last synced: 29 Sep 2026
https://github.com/Cloud-Drift/clouddrift
CloudDrift accelerates the use of Lagrangian data for atmospheric, oceanic, and climate sciences.
climate-data climate-science data-structures oceanography python
Last synced: 29 Sep 2026
https://github.com/DavidLapous/multipers
Python library for multiparameter persistence
cpp cython icml-2024 multiparameter-persistence neurips-2023 persistent-homology python tda topological-data-analysis
Last synced: 29 Sep 2026
https://github.com/ropensci/aorsf
Accelerated Oblique Random Survival Forests
data-science oblique random-forest rstats survival
Last synced: 29 Sep 2026
https://github.com/lanl/scico
Scientific Computational Imaging COde
admm computational-imaging convex-optimization fista inverse-problems jax optimization plug-and-play-priors proximal-algorithms proximal-operators total-variation
Last synced: 29 Sep 2026
https://github.com/betteridiot/bamnostic
a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool
Last synced: 29 Sep 2026
https://github.com/trixi-framework/TrixiParticles.jl
TrixiParticles.jl: Particle-based multiphysics simulations in Julia
julia multiphysics simulation smoothed-particle-hydrodynamics sph
Last synced: 29 Sep 2026
https://github.com/a-slide/pycoQC
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
computing-metrics generates-plots jupyter-notebook nanopore
Last synced: 29 Sep 2026
https://github.com/UNSW-CEEM/nempy
A Python package for modelling the Australian National Electricity Market dispatch procedure
Last synced: 29 Sep 2026
https://github.com/openscm/pymagicc
Python wrapper for the simple climate model MAGICC
climate-model magicc-model python-wrapper
Last synced: 29 Sep 2026
https://github.com/ImperialCollegeLondon/sharpy
Simulation of High Aspect Ratio aeroplanes and wind turbines in Python: a nonlinear aeroelastic code
aeroelasticity aeronautics simulation structural-dynamics structures wind-turbines
Last synced: 29 Sep 2026
https://github.com/DeepRank/pdb2sql
Fast and versatile biomolecular structure PDB file parser using SQL queries
Last synced: 29 Sep 2026
https://github.com/openeventdata/mordecai
Full text geoparsing as a Python library
geocoding geonames geoparsing nlp spacy toponym-resolution
Last synced: 29 Sep 2026
https://github.com/danielenricocahall/elephas
Distributed Deep learning with Keras & Spark
Last synced: 29 Sep 2026
https://github.com/netsiphd/netrd
A library for network {reconstruction, distances, dynamics}
Last synced: 29 Sep 2026
https://github.com/oekosheri/GB_code
A grain boundary generation code
crystallography grain-boundaries high-throughput-computing linear-algebra python
Last synced: 29 Sep 2026
https://github.com/dianna-ai/dianna
Deep Insight And Neural Network Analysis
explainable-artificial-intelligence scientific-research
Last synced: 29 Sep 2026
https://gitlab.com/jesseds/apav
APAV (Atom Probe Analysis and Visualization) is a Python library for the analysis and visualization of atom probe tomography experiments.
Atom Probe Field Evaporation data analysis science tomography
Last synced: 29 Sep 2026
https://github.com/Eden-Kramer-Lab/spectral_connectivity
Frequency domain estimation and functional and directed connectivity analysis tools for electrophysiological data
brain-connectivity canonical-coherence coherence connectivity-measures electrophysiology frequency-domain global-coherence multitaper neuroscience phase-lag-index python spectral-granger-causality spectrogram
Last synced: 29 Sep 2026
https://github.com/OpenGeoVis/PVGeo
🌍 Python package of VTK-based algorithms to analyze geoscientific data and models
3d data-visualization geophysics geosciences model-building open-science paraview paraview-plugin python visual-data-integration visualization vtk
Last synced: 29 Sep 2026
https://github.com/CederGroupHub/smol
Statistical Mechanics on Lattices
cluster-expansion ising-model lattice-gas materials-science monte-carlo statistical-mechanics
Last synced: 29 Sep 2026
https://github.com/MDAnalysis/solvation-analysis
A comprehensive tool for analyzing liquid solvation structure.
Last synced: 29 Sep 2026
https://github.com/BohndiekLab/patato
PATATO: A Python PhotoAcoustic Tomography Analysis Toolkit
Last synced: 29 Sep 2026
https://github.com/CSBiology/FSharpGephiStreamer
F# functions for streaming any kind of graph/network data to the network visualization tool gephi
data-analysis exploratory-data-analysis fsharp gephi graph-visualization streaming-graph-data visualization
Last synced: 29 Sep 2026
https://github.com/grf-labs/policytree
Policy learning via doubly robust empirical welfare maximization over trees
causal-inference policy-learning
Last synced: 29 Sep 2026
https://github.com/beringresearch/ivis
Dimensionality reduction in very large datasets using Siamese Networks
data-visualization dimensionality-reduction machine-learning neural-network siamese-neural-network
Last synced: 29 Sep 2026
https://github.com/AstraZeneca/kallisto
Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.
chemistry computational-chemistry machinelearning quantum-chemistry
Last synced: 29 Sep 2026
https://github.com/ropensci/phylogram
Dendrograms for Evolutionary Analysis
peer-reviewed r r-package rstats
Last synced: 29 Sep 2026
https://github.com/Ciela-Institute/caustics
A gravitational lensing simulator for the machine learning era.
gravitational-lensing pytorch
Last synced: 29 Sep 2026
https://github.com/nasa/ncompare
Compare the structure of two netCDF (or HDF5) files
data-comparison hierarchical-data netcdf
Last synced: 29 Sep 2026
https://github.com/mad-lab-fau/BioPsyKit
A Python package for the analysis of biopsychological data.
acute-stress amylase biomarkers biosignals cortisol ecg-processing health-psychology psychology python questionnaires statistics stress-protocols
Last synced: 29 Sep 2026
https://github.com/jbytecode/JMcDM
A package for Multiple criteria decision-making techniques in Julia
julia mcdm multiple-criteria-decision-making optimization
Last synced: 29 Sep 2026
https://github.com/openpharma/rbmi
Reference based multiple imputation R package
Last synced: 29 Sep 2026
https://github.com/schochastics/netrankr
An R package for network centrality
network-analysis network-centrality r-package
Last synced: 29 Sep 2026
https://github.com/MLMI2-CSSI/foundry
Simplifying the discovery and usage of machine-learning ready datasets in materials science and chemistry
chemistry data-science datasets machine-learning materials-science
Last synced: 29 Sep 2026
https://github.com/CliMA/CalibrateEmulateSample.jl
Stochastic Optimization, Learning, Uncertainty and Sampling
Last synced: 29 Sep 2026
https://github.com/HBClab/NiBetaSeries
Nipype implementation of BetaSeries Correlations (Beta)
Last synced: 29 Sep 2026
https://github.com/ElektraInitiative/libelektra
Elektra serves as a universal and secure framework to access configuration settings in a global, hierarchical key database.
administrator c c-plus-plus configuration configuration-files configuration-management configuration-parser elektra key-database
Last synced: 29 Sep 2026
https://github.com/nasa/prog_models
The NASA Prognostic Model Package is a Python framework focused on defining and building models for prognostics (computation of remaining useful life) of engineering systems, and provides a set of prognostics models for select components developed within this framework, suitable for use in prognostics applications for these components.
modeling prognostic-models prognostics prognostics-health-management simulation
Last synced: 29 Sep 2026
https://github.com/mikahama/uralicNLP
An NLP library for Uralic languages such as Finnish, Skolt Sami, Moksha and so on. Also supporting some non-Uralic languages such as Spanish, French, Arabic, Swedish, Norwegian, Russian and English. LLMs, FSTs and More!
clustering conll-u constraint-grammar dutch finnish french fst german large-language-model lemmatizer llm moksha morphological-analysis morphological-generation nlp-library russian sami spanish swedish uralic-languages
Last synced: 29 Sep 2026
https://github.com/minaskar/pocomc
pocoMC: A Python implementation of Preconditioned Monte Carlo for accelerated Bayesian Computation
astronomy astrophysics bayesian-inference black-box-bayesian-inference cosmology cosmology-inference general-purpose inference machine-learning mcmc mcmc-sampler normalizing-flows probabilistic-data-analysis python sampling sampling-methods smc
Last synced: 29 Sep 2026
https://github.com/mcdc-project/mcdc
A Python-based Monte Carlo radiation transport code
monte-carlo nuclear-engineering particle-transport radiation-transport
Last synced: 29 Sep 2026
https://github.com/SatelliteShorelines/CoastSeg
An interactive toolbox for downloading satellite imagery, applying image segmentation models, mapping shoreline positions and more. The mapping extension for CoastSat and Zoo.
colab earth-engine jupyter landsat python
Last synced: 29 Sep 2026
https://github.com/geodynamics/burnman
BurnMan is a Python toolkit for planetary geophysics, geochemistry and thermodynamics
Last synced: 29 Sep 2026
https://github.com/thepetabyteproject/your
Your Unified Reader
fast-radio-bursts filterbank psrdada psrdada-python psrfits pulsars python
Last synced: 29 Sep 2026
https://github.com/lrnv/cort
Classes and Tools For Some Empirical and Non-parametrical Copula Models.
Last synced: 29 Sep 2026
https://gitlab.com/utopia-project/dantro
dantro is a python package for handling, transforming, and visualizing hierarchically organized data. Integrated into data-intensive projects, it supplies an easy way to define a customizable, configuration-based data processing pipeline. See [utopya](https://gitlab.com/utopia-project/utopya) for an example.
data processing pipeline h5py matplotlib numpy python utopia-project xarray yaml
Last synced: 29 Sep 2026
https://github.com/gboeing/osmnx/
Download, model, analyze, and visualize street networks and other geospatial features from OpenStreetMap.
geography geospatial gis mapping networks networkx openstreetmap osm osmnx overpass-api python routing spatial spatial-analysis spatial-data street-networks transport transportation urban urban-planning
Last synced: 30 Sep 2026
https://github.com/highamm/sptotal
Package for Fitting Spatial Linear Models and Predicting Total Abundances for Finite Populations
Last synced: 29 Sep 2026
https://github.com/MFaymon/spINAR
Semiparametric and parametric estimation and bootstrapping of integer-valued autoregressive (INAR) models.
bootstrapping count-data parametric-estimation penalization semiparametric-estimation simulation time-series validation
Last synced: 29 Sep 2026
https://github.com/johentsch/ms3
A parser for annotated MuseScore 3 files.
corpus corpus-data corpus-generator corpus-processing corpus-tools musescore musescore2 musescore3 musescore4 music-score music-scores parser sheet-music sheet-music-parser tsv tsv-files tsv-format xml-parser xml-parser-library xml-parsing
Last synced: 29 Sep 2026
https://github.com/ropensci/opentripplanner
An R package to set up and use OpenTripPlanner (OTP) as a local or remote multimodal trip planner.
data isochrones java opentripplanner otp public-transport r routing transport transportation-planning
Last synced: 29 Sep 2026
https://github.com/miykael/atlasreader
Python interface for generating coordinate tables and region labels from statistical MRI images
Last synced: 30 Sep 2026
https://github.com/konfound-project/konfound
R package for carrying out sensitivity analysis
Last synced: 29 Sep 2026
https://github.com/arives/rr2
R2 for correlated data; see https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syy060/5098616
Last synced: 29 Sep 2026
https://github.com/steven-murray/powerbox
A python package for making arbitrarily structured, arbitrary-dimension boxes
Last synced: 29 Sep 2026
https://github.com/EnvModellingGroup/hrds
Hierarchical raster data set: smooth interpolation of raster files at different resolutions for multiscale modelling
gis modelling numerical-modelling science-research
Last synced: 29 Sep 2026
https://github.com/RAMP-project/RAMP
Repository of the open-source RAMP model for generating multi-energy loads profiles
Last synced: 29 Sep 2026
https://github.com/AndreWeiner/flowtorch
flowTorch - a Python library for analysis and reduced-order modeling of fluid flows
csv dmd jupyter openfoam pod pytorch spod tau
Last synced: 29 Sep 2026
https://github.com/PaulSt/NGSTrefftz
Add-On to NGSolve for Trefftz methods
finite-element-method numerical-methods open-source trefftz-methods
Last synced: 29 Sep 2026
https://github.com/NVlabs/scene_synthesizer
Python package to create manipulation scenes.
Last synced: 29 Sep 2026
https://github.com/PRIDE-Archive/pridepy
Python client for PRIDE Archive Rest API.
mass-spectrometry pride pride-database proteomics python python-client
Last synced: 29 Sep 2026
https://github.com/Sm00thix/IKPLS
Fast CPU and GPU Python implementations of Improved Kernel Partial Least Squares (PLS) by Dayal and MacGregor (1997) and Fast Partition-Based Cross-Validation With Centering and Scaling for XTX and XTY by Engstrøm and Jensen (2025). This package also includes options to use sample weights for PLS modeling.
algorithm data-science gpu-support linear-regression partial-least-squares partial-least-squares-regression pls plsda plsr tpu-acceleration weighted-least-squares weighted-linear-regression weighted-regression
Last synced: 29 Sep 2026
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