Collections: JOSS
https://github.com/fstrozzi/bioruby-pipengine
An ultra light YAML-based pipeline execution engine
Last synced: 29 Sep 2026
https://github.com/prioritizr/wdpar
Interface to the World Database on Protected Areas
biodiversity conservation cran data database protected-areas r r-package rstats spatial
Last synced: 29 Sep 2026
https://github.com/alan-turing-institute/autoemulate
Emulate simulations easily
active-learning aiphys calibration emulation ensemble gaussian-processes history-matching hut23 hut23-1468 mcmc neural-networks pytorch sensitivity-analysis uncertainty-quantification
Last synced: 29 Sep 2026
https://github.com/dynamicslab/pykoopman
A package for computing data-driven approximations to the Koopman operator.
Last synced: 29 Sep 2026
https://github.com/thieu1995/permetrics
Artificial intelligence (AI, ML, DL) performance metrics implemented in Python
classification classification-report clustering-evaluation coefficient-of-determination deviation-of-runoff-volume evaluation-metrics kling-gupta-efficiency mae nash-sutcliffe-efficiency performance-metrics regression regression-methods relative-error rmse symmetric-mean-absolute-percentage willmott-index
Last synced: 29 Sep 2026
https://github.com/stemangiola/tidyHeatmap
Draw heatmap simply using a tidy data frame
brewer complexheatmap custom-palette dplyr graphviz heatmap mtcars plotting r rstudio scale tibble tidy tidy-data-frame tidybulk tidyverse viridis
Last synced: 29 Sep 2026
https://github.com/earth-chris/elapid
Species distribution modeling tools, including a python implementation of Maxent
biodiversity-informatics biogeography geospatial maxent niche-modelling species-distribution-modelling
Last synced: 29 Sep 2026
https://github.com/NorskRegnesentral/shapr
Explaining the output of machine learning models with more accurately estimated Shapley values
explainable-ai explainable-ml rcpp rcpparmadillo rstats shapley
Last synced: 29 Sep 2026
https://github.com/open-atmos/PyMPDATA
Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia, Rust and Matlab
advection advection-diffusion atmospheric-modelling numba numerical-integration pde-solver pypi-package python research simulation
Last synced: 29 Sep 2026
https://github.com/NatLabRockies/bifacial_radiance
Toolkit for working with RADIANCE for the ray-trace modeling of Bifacial Photovoltaics
bifacial gui photovoltaics radiance renewable-energy renewables
Last synced: 29 Sep 2026
https://github.com/actris-cloudnet/cloudnetpy
Python package for Cloudnet data processing
Last synced: 29 Sep 2026
https://github.com/NCAS-CMS/cfdm
A Python reference implementation of the CF data model
aggregation atmosphere cf climate dask data data-compression forecasting metadata netcdf ocean python ugrid zarr
Last synced: 29 Sep 2026
https://github.com/inpefess/gym-saturation
a collection of Gymnasium environments for saturation provers
Last synced: 29 Sep 2026
https://github.com/LiberTEM/LiberTEM
Open pixelated STEM framework
data-processing electron-microscopy image-processing python
Last synced: 29 Sep 2026
https://github.com/sciris/sciris
Fast, flexible tools to simplify scientific Python
computational-science containers data-science matplotlib numpy parallelization plotting python scientific-computing utilities
Last synced: 29 Sep 2026
https://github.com/ropensci/PostcodesioR
API wrapper around postcodes.io - free UK postcode lookup and geocoder
api-wrapper geocoder geographic-data peer-reviewed postcode r r-package rstats uk
Last synced: 29 Sep 2026
https://github.com/FZJ-IEK3-VSA/FINE
The ETHOS.FINE python package provides a framework for modeling, optimizing and assessing energy systems
Last synced: 29 Sep 2026
https://github.com/spglib/spgrep
On-the-fly generator of space-group irreducible representations
crystallography group-theory irreducible-representations materials-science python representation-theory
Last synced: 29 Sep 2026
https://github.com/virgesmith/UKCensusAPI
UK Census Data queries and downloads from python or R
data-science python r
Last synced: 29 Sep 2026
https://github.com/PyAutoLabs/PyAutoGalaxy
PyAutoGalaxy: Open-Source Multiwavelength Galaxy Structure & Morphology
astronomy astrophysics galaxies image-processing morphology python
Last synced: 29 Sep 2026
https://github.com/MTgeophysics/mtpy
[DEPRECATED] Python toolbox for standard Magnetotelluric (MT) data analysis
Last synced: 30 Sep 2026
https://github.com/PeteHaitch/GenomicTuples
Representation and Manipulation of Genomic Tuples in R
Last synced: 29 Sep 2026
https://github.com/qiskit-community/qiskit-dynamics
DEPRECATED - Tools for building and solving models of quantum systems in Qiskit
Last synced: 29 Sep 2026
https://github.com/bessagroup/f3dasm
Framework for Data-Driven Design & Analysis of Structures & Materials (F3DASM)
computational-mechanics data-driven design-of-experiments framework machine-learning materials-science
Last synced: 29 Sep 2026
https://github.com/jmejia8/Metaheuristics.jl
High-performance metaheuristics for optimization coded purely in Julia.
constrained-optimization decision-making differential-evolution hypervolume multi-objective-optimization nsga2 optimization pso simulated-annealing
Last synced: 29 Sep 2026
https://github.com/cvs-health/langfair
LangFair is a Python library for conducting use-case level LLM bias and fairness assessments
ai ai-safety artificial-intelligence bias bias-detection ethical-ai fairness fairness-ai fairness-ml fairness-testing large-language-models llm llm-evaluation llm-evaluation-framework llm-evaluation-metrics python responsible-ai
Last synced: 29 Sep 2026
https://gitlab.com/moorepants/skijumpdesign
A ski jump design tool for equivalent fall height. Includes a library for 2D skiing simulations and a graphical web application for designing ski jumps.
design jump simulation ski snowboard sports terrain park
Last synced: 29 Sep 2026
https://github.com/HypothesisWorks/hypothesis/
The property-based testing library for Python
fuzzing property-based-testing python testing
Last synced: 29 Sep 2026
https://github.com/jonescompneurolab/hnn-core
Simulation and optimization of neural circuits for MEG/EEG source estimates
computational-modeling eeg meg neuron-simulator
Last synced: 29 Sep 2026
https://github.com/martin3141/spant
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data
brain cran mri mrs mrshub spectroscopy
Last synced: 29 Sep 2026
https://github.com/OnroerendErfgoed/atramhasis
An online SKOS editor
app pypi-package python skos thesaurus vocabulary
Last synced: 29 Sep 2026
https://github.com/simpeg/aurora
software for processing natural source electromagnetic data
Last synced: 29 Sep 2026
https://github.com/JuliaEarth/GeoStats.jl
An extensible framework for geospatial data science and geostatistical modeling fully written in Julia
datascience geo geomodeling geospatial geostatistics gis spatial-statistics statistical-learning statistics
Last synced: 29 Sep 2026
https://github.com/vivo-project/VIVO
VIVO is an extensible semantic web application for research discovery and showcasing scholarly work
Last synced: 29 Sep 2026
https://github.com/bjodah/pyneqsys
Solve symbolically defined systems of non-linear equations numerically.
least-squares nonlinear-equations root-finding symbolic-manipulation sympy
Last synced: 29 Sep 2026
https://github.com/daffidwilde/matching
A package for solving matching games
gale-shapley game-theory hospital-residents matching-game matching-problems stable-marriage
Last synced: 29 Sep 2026
https://github.com/bcgov/bcdata
An R package for searching & retrieving data from the B.C. Data Catalogue
bcdc citz data-science env r r-package rstats
Last synced: 29 Sep 2026
https://github.com/vortex-exoplanet/VIP
VIP is a python package/library for angular, reference star and spectral differential imaging for exoplanet/disk detection through high-contrast imaging.
data-processing extrasolar-planets-disks high-contrast-imaging image-processing low-rank-approximation mcmc pca
Last synced: 29 Sep 2026
https://github.com/PieterjanRobbe/GaussianRandomFields.jl
A package for Gaussian random field generation in Julia
Last synced: 29 Sep 2026
https://github.com/ralna/GALAHAD
A library of modern Fortran modules for nonlinear optimization
c cubic-regularization-methods fortran julia mathematical-programming matlab nonlinear-least-squares nonlinear-optimization numerical-optimization python quadratic-programming trust-region-methods
Last synced: 29 Sep 2026
https://github.com/kgjerde/corporaexplorer
An R package for dynamic exploration of text collections
corpora corpus r shiny text-analysis
Last synced: 29 Sep 2026
https://github.com/pyplati/platipy
Processing Library and Analysis Toolkit for Medical Imaging in Python
image-analysis medical-imaging python registration segmentation visualization
Last synced: 29 Sep 2026
https://gitlab.com/emd-dev/emd
Empirical Mode Decomposition in Python <a href="https://gitlab.com/ajquinn/emd/commits/master"><img alt="pipeline status" src="https://gitlab.com/ajquinn/emd/badges/master/pipeline.svg" /></a>
Last synced: 29 Sep 2026
https://github.com/Natsiopoulos/ARDL
ARDL, ECM and Bounds-Test for Cointegration
Last synced: 29 Sep 2026
https://github.com/paucablop/chemotools
The scikit-learn-native foundation package for chemometrics 🧪 🤖
artificial-intelligence autoencoders chemometrics deep-learning hacktoberfest ir-spectroscopy machine-learning multivariate-analysis nir-spectroscopy python raman-spectroscopy scikit-learn sklearn spectra spectroscopy
Last synced: 29 Sep 2026
https://github.com/lilyminium/psiresp
RESP with inter- and intra-molecular constraints in Psi4.
atomic-charges molecular-dynamics psi4 python
Last synced: 29 Sep 2026
https://github.com/cdslaborg/paramonte
ParaMonte: Parallel Monte Carlo and Machine Learning Library for Python, MATLAB, Fortran, C++, C.
adaptive-learning bayesian-inference bayesian-statistics c cpp fortran machine-learning machine-learning-algorithms machine-learning-library markov-chain matlab mcmc monte-carlo monte-carlo-simulations mpi numerical-integration openmp python sampling
Last synced: 29 Sep 2026
https://github.com/CMakePP/CMinx
Generates API documentation for CMake functions and macros
cmake documentation-tool
Last synced: 29 Sep 2026
https://github.com/gacou54/pyorthanc
Python library that wrap the Orthanc REST API and facilitate the manipulation of data in Orthanc
Last synced: 29 Sep 2026
https://github.com/pynucastro/pynucastro
a python library for nuclear astrophysics
Last synced: 29 Sep 2026
https://github.com/nansencenter/DAPPER
Data Assimilation with Python: a Package for Experimental Research
bayesian-filter bayesian-methods chaos data-assimilation enkf kalman kalman-filtering particle-filter state-estimation
Last synced: 29 Sep 2026
https://github.com/sambitdash/PDFIO.jl
PDF Reader Library for Native Julia.
julia pdf pdf-development pdf-document pdf-files pdf-library pdf-specification text-extraction
Last synced: 29 Sep 2026
https://github.com/SciML/GlobalSensitivity.jl
Robust, Fast, and Parallel Global Sensitivity Analysis (GSA) in Julia
differential-equations efast global-sensitivity-analysis gsa julia julia-language julialang morris-method ode ordinary-differential-equations scientific-machine-learning sciml sensitivity-analysis sobol-method
Last synced: 29 Sep 2026
https://github.com/ronikobrosly/causal-curve
A python package with tools to perform causal inference using observational data when the treatment of interest is continuous.
Last synced: 29 Sep 2026
https://github.com/RadioAstronomySoftwareGroup/pyradiosky
Python objects and interfaces for representing diffuse, extended and compact astrophysical radio sources
Last synced: 29 Sep 2026
https://github.com/coleygroup/pyscreener
pythonic interface to virtual screening software
computational-biology distributed-computing molecular-docking ray virtual-screening
Last synced: 29 Sep 2026
https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl
Import, process and interpret geophysical data sets to be used in numerical models.
Last synced: 29 Sep 2026
https://github.com/ml-evs/matador
⚗️ matador is an aggregator, manipulator and runner of first-principles calculations, written with a bent towards battery 🔋 electrode materials.
computational-chemistry materials-science python
Last synced: 29 Sep 2026
https://github.com/RWTH-EBC/FiLiP
FIWARE Library for Python (FiLiP) to work with FIWARE API
fiware fiware-iot-agents fiware-ngsi-v2 fiware-orion fiware-quantum-leap hacktoberfest iot maintained python tool
Last synced: 29 Sep 2026
https://github.com/DeepRegNet/DeepReg
Medical image registration using deep learning
convolutional-neural-networks deep-learning deep-neural-networks deepreg image-fusion image-registration medical-image-registration neural-network tensorflow2
Last synced: 29 Sep 2026
https://github.com/jameschapman19/cca_zoo
Canonical Correlation Analysis Zoo: A collection of Regularized, Deep Learning based, Kernel, and Probabilistic methods in a scikit-learn style framework
canonical-correlation-analysis cca cca-zoo dcca deep kernel multiset-cca multiview pls pytorch tensor-cca
Last synced: 29 Sep 2026
https://github.com/PhilBoileau/scPCA
A toolbox for sparse contrastive principal component analysis
bioconductor contrastive-learning dimensionality-reduction
Last synced: 29 Sep 2026
https://github.com/samreay/ChainConsumer
Corner plots, LaTeX tables and plotting walks.
Last synced: 29 Sep 2026
https://github.com/KVSlab/morphMan
A collection of tools for manipulation of morphological features in patient-specific geometries
biomedical geometric-algorithms morphology vascular
Last synced: 29 Sep 2026
https://github.com/xarray-contrib/xeofs
Comprehensive EOF analysis in Python with xarray: A versatile, multidimensional, and scalable tool for advanced climate data analysis
climate-science dask dimensionality-reduction eof-analysis pattern-recognition pca xarray
Last synced: 29 Sep 2026
https://github.com/underworldcode/stripy
2D spherical and Cartesian triangulation toolkit using tripack, stripack, srfpack and ssrfpack
fortran meshes python spherical-geometry triangulation-delaunay
Last synced: 29 Sep 2026
https://github.com/UM-Bridge/umbridge
UM-Bridge (the UQ and Model Bridge) provides a unified interface for numerical models that is accessible from virtually any programming language or framework.
Last synced: 29 Sep 2026
https://github.com/pangeo-data/climpred
:earth_americas: Verification of weather and climate forecasts :earth_africa:
climate climate-analysis dask forecasting pangeo prediction python s2d s2s xarray
Last synced: 29 Sep 2026
https://github.com/UCBerkeleySETI/blimpy
Breakthrough Listen I/O Methods for Python
Last synced: 29 Sep 2026
https://github.com/xoopR/set6
R6 object-oriented interface for mathematical sets.
intervals oop r r6 sets
Last synced: 29 Sep 2026
https://github.com/copasi/basico
A simplified python interface to COPASI.
copasi python
Last synced: 29 Sep 2026
https://github.com/derrynknife/SurPyval
A Python package for survival analysis. The most flexible survival analysis package available. SurPyval can work with arbitrary combinations of observed, censored, and truncated data. SurPyval can also fit distributions with 'offsets' with ease, for example the three parameter Weibull distribution.
actuarial-science churn-prediction non-parametric parametric-distribution parametric-methods probability-plot reliability reliability-analysis reliability-engineering risk-analysis survival-analysis weibull
Last synced: 29 Sep 2026
https://github.com/singularityhub/singularity-hpc
Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.
containers hpc lmod reproducibility singularity
Last synced: 29 Sep 2026
https://github.com/ytree-project/ytree
A Python package for analyzing tree data and especially merger trees.
analysis astronomy astrophysics data merger-trees python simulations trees
Last synced: 29 Sep 2026
https://github.com/toruseo/UXsim
Vehicular traffic flow simulator in road network for Python
dynamic-traffic-assignment simulation traffic traffic-flow traffic-flow-simulation traffic-simulation transportation transportation-network
Last synced: 29 Sep 2026
https://github.com/TomKellyGenetics/graphsim
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
benchmarking gene-expression gene-regulatory-networks genetics genomic-data-analysis genomics graph-algorithms igraph-networks joss ngs-analysis package r-stats simulated-data simulation-modeling
Last synced: 29 Sep 2026
https://github.com/SchlossLab/mikropml
User-Friendly R Package for Supervised Machine Learning Pipelines
machine-learning r-package rstats
Last synced: 29 Sep 2026
https://gitlab.com/open-darts/open-darts
The DARTS framework is designed for forward and inverse modeling in geo-energy applications.
energy transition geothermal energy production modeling of CO2 sequestration
Last synced: 29 Sep 2026
https://github.com/ellessenne/comorbidity
An R package for computing comorbidity scores.
comorbidity r rstats
Last synced: 29 Sep 2026
https://github.com/lrnv/Copulas.jl
A fully `Distributions.jl`-compliant copula package
copula julia
Last synced: 29 Sep 2026
https://github.com/USCbiostats/fmcmc
A friendly MCMC framework
adaptive bayesian-inference markov-chain-monte-carlo mcmc metropolis-hastings parallel-computing r r-package
Last synced: 29 Sep 2026
https://github.com/ropensci/stats19
R package for working with open road traffic casualty data from Great Britain
r r-package rstats
Last synced: 29 Sep 2026
https://github.com/obss/jury
Comprehensive NLP Evaluation System
datasets evaluate evaluation huggingface machine-learning metrics natural-language-processing nlp nlp-evaluation python pytorch transformers
Last synced: 29 Sep 2026
https://github.com/galsci/pysm
PySM 3: Sky emission simulations for Cosmic Microwave Background experiments
cosmic-microwave-background cosmology healpix healpy mpi python
Last synced: 29 Sep 2026
https://github.com/ConorMacBride/mcalf
MCALF: Multi-Component Atmospheric Line Fitting
astronomy python solar solar-physics sun
Last synced: 29 Sep 2026
https://github.com/fabian-sp/GGLasso
A Python package for General Graphical Lasso computation
graphical-lasso graphical-models latent-variable-models network-inference optimization
Last synced: 29 Sep 2026
https://github.com/FraunhoferIWES/foxes
Farm Optimization and eXtended yield Evaluation Software
Last synced: 29 Sep 2026
https://github.com/dgbowl/yadg
yadg: yet another datagram
batteries catalysis chromatography data-science electrochemistry parser
Last synced: 29 Sep 2026
https://github.com/swiftsim/swiftsimio
Python library for reading SWIFT data. Uses unyt and h5py.
astrophysics cosmology hdf5 particle simulation sph
Last synced: 29 Sep 2026
https://gitlab.com/remram44/taguette
Free and open source qualitative research tool
document hacktoberfest highlights notes qual qualitative research tagging tags text
Last synced: 29 Sep 2026
https://github.com/nextstrain/nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus
Last synced: 29 Sep 2026
https://github.com/cjbarrie/academictwitteR
Repo for academictwitteR package to query the Twitter Academic Research Product Track v2 API endpoint.
r r-package twitter twitter-api
Last synced: 29 Sep 2026
https://github.com/davidpagnon/Sports2D
Compute 2D human pose and angles from a video or a webcam.
biomechanics blazepose coaching joint-angles kinematics kinovea markerless openpose pose-estimation rtmpose sports sports-analytics
Last synced: 29 Sep 2026
https://github.com/stfbnc/fathon
python package for DFA (Detrended Fluctuation Analysis) and related algorithms
dcca detrended-fluctuation-analysis dfa hurst-exponent mfdfa multifractal-analysis multifractal-detrended-fluctuation multifractal-spectrum python scientific-software
Last synced: 29 Sep 2026
https://github.com/MREYE-LUMC/ZOSPy
Wrapper around the Zemax OpticStudio API. Provides a more pythonic and intuitive way to interact with the ZOS-API through python using a .NET connection.
optics optics-simulation opticstudio python zemax zos-api
Last synced: 29 Sep 2026
https://gitlab.com/materials-modeling/wulffpack
[A package for Wulff constructions.](https://wulffpack.materialsmodeling.org)
Wullf construction atomic structure nanoparticles surface energy surfaces thermodynamics
Last synced: 29 Sep 2026
https://github.com/pboesu/rucrdtw
R Bindings for the UCR Suite for fast time series subsequence search
Last synced: 29 Sep 2026
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