https://github.com/tdaverse/TDAstats
R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.
cran data-science ggplot2 homology homology-calculations homology-computation joss persistent-homology pipeline r r-package r-packages ripser tda topological-data-analysis topology topology-visualization visualization
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/JohnCoene/sigmajs
Σ sigma.js for R
htmlwidgets network-visualization r rstats sigmajs
Last synced: 29 Sep 2026
https://github.com/williamsbenjamin/blendR
Blending a Probablilty Sample and a Non-Probability Sample in a Capture-Recapture Setting
Last synced: 29 Sep 2026
https://github.com/yt-project/unyt
Handle, manipulate, and convert data with units in Python
Last synced: 29 Sep 2026
https://github.com/sdtaylor/pyPhenology
Plant phenology models in python with a scikit-learn inspired API
ecology ecology-modelling plants science
Last synced: 29 Sep 2026
https://github.com/j-andrews7/Genotify
A minimal desktop app for easy and convenient gene annotation and lookup.
bioinformatics desktop-application gene gene-annotation genetics lookup protein-function
Last synced: 29 Sep 2026
https://github.com/loftytopping/PyBox
A box-model that automatically creates and solves equations used to describe the evolution in atmospheric composition using Python with Numba and, optionally, Fortran.
atmospheric-science chemistry fortran numba
Last synced: 29 Sep 2026
https://github.com/bmorris3/aesop
ARC Echelle Spectroscopic Observation Pipeline (aesop)
astronomy python spectroscopy
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/steven-murray/powerbox
A python package for making arbitrarily structured, arbitrary-dimension boxes
Last synced: 29 Sep 2026
https://github.com/emptyport/js-emass
This is a JavaScript implementation of the emass algorithm for calculating accurate isotopic envelopes
Last synced: 29 Sep 2026
https://github.com/gallantlab/cottoncandy
sugar for s3
cloud-storage google-drive numpy-arrays python s3
Last synced: 29 Sep 2026
https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe
RNAsik - more than just a pipeline
Last synced: 29 Sep 2026
https://github.com/dirmeier/datastructures
:rocket: Implementation of core data structures for R
algorithms datastructures r rcpp
Last synced: 29 Sep 2026
https://github.com/pdebuyl-lab/tidynamics
A tiny package to compute the dynamics of stochastic and molecular simulations
correlation molecular-dynamics numpy stochastic-process
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/federeghe/chronovise
Measurement-Based Probabilistic Timing Analysis framework
mbpta real-time research-tool wcet
Last synced: 29 Sep 2026
https://github.com/davidnsousa/bor
Data analysis for field behavior observations of dyadic social interactions
Last synced: 29 Sep 2026
https://github.com/palash1992/GEM
graph-embedding graph-embeddings link-prediction network-embedding network-visualization
Last synced: 29 Sep 2026
https://github.com/lmcinnes/umap
Uniform Manifold Approximation and Projection
dimensionality-reduction machine-learning topological-data-analysis umap visualization
Last synced: 30 Sep 2026
https://github.com/dflemin3/approxposterior
A Python package for approximate Bayesian inference and optimization using Gaussian processes
approximate-inference bayesian-inference bayesian-optimization gaussian-processes inference python
Last synced: 29 Sep 2026
https://github.com/jcmgray/quimb
A python library for quantum information and many-body calculations including tensor networks.
dmrg entanglement mera peps physics python python3 quantum quantum-circuit quantum-circuit-simulator quantum-computing tebd tensor-network tensor-networks tensors
Last synced: 29 Sep 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: 29 Sep 2026
https://github.com/calliope-project/calliope
A multi-scale energy systems modelling framework
energy energy-system optimisation pyomo python
Last synced: 29 Sep 2026
https://github.com/scikit-tda/ripser.py
A Lean Persistent Homology Library for Python
data-science homology persistent-homology ripser tda topological-data-analysis topology
Last synced: 29 Sep 2026
https://github.com/ejhigson/nestcheck
Error analysis, diagnostic tests and plots for nested sampling calculations.
bayesian-inference dynamic-nested-sampling error-analysis nested-sampling python sampling-error
Last synced: 29 Sep 2026
https://github.com/scikit-beam/NeuNorm
Normalization of fits and tiff files
Last synced: 30 Sep 2026
https://github.com/mpascariu/ungroup
Estimating Smooth Distributions from Coarsely Binned Data - R Package
distributions glm smoothing ungrouping
Last synced: 29 Sep 2026
https://github.com/grg2rsr/SeqPeelSort
A spike sorting algorithm for single sensillum recordings
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/boyanangelov/sdmbench
Benchmarking Species Distribution Models
benchmarking ecology machine-learning r sdm
Last synced: 29 Sep 2026
https://github.com/ejhigson/dyPolyChord
Super fast dynamic nested sampling with PolyChord (Python, C++ and Fortran likelihoods).
dynamic-nested-sampling nested-sampling
Last synced: 29 Sep 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: 29 Sep 2026
https://github.com/degauss-org/DeGAUSS
Decentralized Geomarker Assessment for Multi-Site Studies
Last synced: 29 Sep 2026
https://github.com/ejhigson/perfectns
"Perfect" dynamic and standard nested sampling for spherically symmetric likelihoods and priors.
bayesian-inference dynamic-nested-sampling nested-sampling pure-python
Last synced: 29 Sep 2026
https://github.com/volfpeter/localclustering
Python 3 implementation and documentation of the Hermina-Janos local graph clustering algorithm.
cluster cluster-analysis clustering clustering-algorithm graph-algorithms graph-theory hierarchical-clustering local-clustering python python3 ranking social-network-analysis
Last synced: 29 Sep 2026
https://github.com/Benjamin-Lee/CodonAdaptationIndex
Python Implementation of Codon Adaption Index
bioinformatics codons genetics
Last synced: 29 Sep 2026
https://github.com/quanteda/quanteda
An R package for the Quantitative Analysis of Textual Data
corpus natural-language-processing quanteda r text-analytics
Last synced: 30 Sep 2026
https://github.com/atmoschem/EmissV
Create and processing emissions for numeric air quality models
atmos atmospheric-chemistry atmospheric-modelling atmospheric-models atmospheric-science emissions wrf-chem
Last synced: 29 Sep 2026
https://github.com/stulacy/multistateutils
Utility funtions for parametric multi-state modelling in R
Last synced: 29 Sep 2026
https://github.com/raamana/mrivis
medical image visualization library and development toolkit
alignment checkerboard comparison mismatch mri neuroimaging neuroscience quality-control registration similarity visualization
Last synced: 29 Sep 2026
https://github.com/drvinceknight/Nashpy
A python library for 2 player games.
algorithm computer-science equilibria game mathematics nash python
Last synced: 29 Sep 2026
https://github.com/fatiando/verde
Processing and gridding spatial data, machine-learning style
earth-science fatiando-a-terra geophysics geoscience geospatial interpolation machine-learning python python3 scipy scipy-stack
Last synced: 29 Sep 2026
https://github.com/whimian/pyGeoPressure
Pore pressure prediction using seismic velocity and well log data
formation-pressure geomechancis geophysics geopressure pore-pressure-prediction
Last synced: 29 Sep 2026
https://github.com/schalkdaniel/compboost
C++ implementation and R API for componentwise boosting
boosting-framework interpretable-machine-learning machine-learning
Last synced: 29 Sep 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: 29 Sep 2026
https://github.com/hooman650/BioSigKit
BioSignal Analysis Kit
biosignal ecg-qrs-detection ecg-signal matlab pan-tomkins-qrs-detection signal-processing
Last synced: 29 Sep 2026
https://github.com/hamedmx/YAD-ILP-Tool
A Learning-based Inductive Logic Programming Tool
Last synced: 29 Sep 2026
https://github.com/wilsoncai1992/adaptest
Data-adaptive testing under high-dimensions
Last synced: 29 Sep 2026
https://github.com/ropensci/nasapower
API Client for NASA POWER Global Meteorology, Surface Solar Energy and Climatology in R
agroclimatology agroclimatology-data data-access earth-science nasa nasa-power r r-package rstats weather weather-data weather-variables
Last synced: 29 Sep 2026
https://github.com/prestsoftware/prest
Revealed preference analysis and preference estimation from choice datasets
Last synced: 29 Sep 2026
https://github.com/qiime2/q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data.
hacktoberfest
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/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/hippylib/hippylib
An Extensible Software Framework for Large-Scale Inverse Problems
Last synced: 29 Sep 2026
https://github.com/davidnsousa/mcsd
MATLAB/Octave tool for Monte-Carlo simulations of diffusion in biological tissues
Last synced: 29 Sep 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: 29 Sep 2026
https://github.com/vc1492a/PyNomaly
Anomaly detection using LoOP: Local Outlier Probabilities, a local density based outlier detection method providing an outlier score in the range of [0,1].
anomalies anomaly-detection machine-learning nearest-neighbors outlier-detection outlier-scores outliers probability
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/malmaud/TensorFlow.jl
A Julia wrapper for TensorFlow
gpu julia machine-learning tensorflow wrapper
Last synced: 29 Sep 2026
https://github.com/mattgolub/fixed-point-finder
FixedPointFinder: A Tensorflow toolbox for identifying and characterizing fixed points in recurrent neural networks
Last synced: 29 Sep 2026
https://github.com/rrrlw/helixvis
Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.
biochemistry cran helical-wheels peptide-sequences r visualization wenxiang-diagrams
Last synced: 29 Sep 2026
https://github.com/cicirello/JavaPermutationTools
A Java library for computation on permutations and sequences
edit-distance permutation-distance permutation-distance-metrics permutations sequences string-distance
Last synced: 29 Sep 2026
https://github.com/fellstat/ipc
Tools for message passing between processes
Last synced: 29 Sep 2026
https://github.com/gomesdasilva/ACTIN
ACTIN is a Python program to calculate stellar activity indices
exoplanets radial-velocity spectroscopy stellar-activity
Last synced: 29 Sep 2026
https://github.com/oxinabox/DataDepsGenerators.jl/
Utility for developers to help define DataDeps registration blocks, for reusing existing Data with DataDeps.jl
data-management opendata openscience
Last synced: 29 Sep 2026
https://github.com/simonGreenhill/Treemaker
A Python library for creating a Newick formatted tree from a set of classification strings
classification newick newick-format phylogenetics python taxonomy
Last synced: 29 Sep 2026
https://github.com/otiai10/hotsub
Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
aws batch-job bioinformatics cwl cwl-workflow docker docker-machine etl-framework gcp wdl wdl-workflow workflow workflow-engine
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/spectralDNS/shenfun
High performance computational platform in Python for the spectral Galerkin method
chebyshev curvilinear-coordinates cylindrical-coordinates fenics fourier galerkin hermite hpc laguerre legendre mobius polar-coordinates python spectral spectral-methods spherical-coordinates turbulence ultraspherical
Last synced: 29 Sep 2026
https://github.com/raphaelvallat/pingouin
Statistical package in Python based on Pandas
anova bayesian-statistics circular-statistics cohens-d correlations effect-size multiple-comparisons pandas statistical-methods statistical-tests statistics ttest
Last synced: 30 Sep 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: 29 Sep 2026
https://github.com/ropensci/rcites
:package: R package to access the CITES Speciesplus database
api-client cites database endangered-species r r-package rstats trade
Last synced: 29 Sep 2026
https://bitbucket.org/cdegroot/wediff
WEdiff Automatic Differentiation Library
Last synced: 29 Sep 2026
https://github.com/ejolly/pymer4
All the convenience of lme4 in python
lme4 mixed-models python
Last synced: 29 Sep 2026
https://github.com/cMadan/ElGateau
ElGateau: A Library for Using the Elgato Stream Deck for Experimental Psychology Research
Last synced: 29 Sep 2026
https://github.com/stgl/scarplet
Topographic edge detection of fault scarps and other landforms in digital elevation data
dem fault-scarps feature-detection signal-processing template-matching
Last synced: 29 Sep 2026
https://github.com/ropensci/restez
:sleeping: :open_file_folder: Create and Query a Local Copy of GenBank in R
dna entrez genbank r r-package rstats sequence
Last synced: 29 Sep 2026
https://github.com/MikeHeiber/Ising_OPV
A C++ software tool for generating and analyzing model bulk heterojunction morphologies in a parallel computing environment
materials-science organic-semiconductors
Last synced: 29 Sep 2026
https://github.com/maxrousseau/pfla
pfla: Python Facial Landmark Analysis
computer-vision machine-learning medical-image-processing statistics
Last synced: 29 Sep 2026
https://github.com/AlexPof/opycleid
Opycleid - A Python package for transformational music theory
algebraic-structures category-theory chords mathematics music-theory python3
Last synced: 29 Sep 2026
https://github.com/equib/proEQUIB
proEQUIB - IDL/GDL Library for Plasma Diagnostics and Abundance Analysis
atomic-level-populations chemical-elements gdl idl idl-library line-emissivities proequib statistical-equilibrium
Last synced: 29 Sep 2026
https://github.com/garretrc/ggvoronoi
Easy Voronoi diagram heatmaps with ggplot2
Last synced: 29 Sep 2026
https://github.com/sumbose/iRF
iterative Random Forests (iRF): iteratively grows weighted random forests, finds interaction among features
Last synced: 29 Sep 2026
https://github.com/masspastore/overlapping
Estimation of Overlapping in Empirical Distributions.
package r
Last synced: 29 Sep 2026
https://github.com/wino6687/SWEpy
Python library for scraping, subsetting, and concatenating temperature brightness data for analyzing SWE.
Last synced: 29 Sep 2026
https://github.com/romunov/wolfexplorer
Explorer designed to visualize complex multi-year multi-specimen data. Case study of Slovenian wolves.
animals cartography genetics mcp parentage r samples shiny shinydashboard wolves
Last synced: 29 Sep 2026
https://github.com/jmborr/idpflex
Analysis of intrinsically disordered proteins by comparing MD simulations to Small Angle Scattering experiments
intrinsically-disordered lmfit md neutron proteins sans saxs scattering simulations
Last synced: 29 Sep 2026
https://github.com/GPUE-group/GPUE
GPU Gross-Pitaevskii Equation numerical solver for Bose-Einstein condensates.
cuda fft gpu numerical-calculations physics quantum-mechanics research simulation superfluid
Last synced: 29 Sep 2026
https://github.com/wimvanderbauwhede/RefactorF4Acc
An Automated Fortran Code Refactoring Tool to Facilitate Acceleration of Numerical Simulations
Last synced: 29 Sep 2026
https://github.com/RuleBasedIntegration/JOSS-Publication
Text-sources for the publication of Rubi in the Journal of Open-Source Software
Last synced: 29 Sep 2026
https://github.com/telegraphic/hickle
a HDF5-based python pickle replacement
Last synced: 29 Sep 2026
https://github.com/KVSlab/bloodflow
Implementation of the 1D blood flow equations using FEniCS
Last synced: 29 Sep 2026
https://github.com/kpeeters/cadabra2
A field-theory motivated approach to computer algebra.
cadabra2 computer-algebra computer-algebra-system cplusplus mathematics physics python3 science-research symbolic-manipulation sympy tensor-algebra tensors
Last synced: 29 Sep 2026
