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ORCIDJournal of Open Source Software, Volume 7
Volume 7, Number 69, January 2022
- Eike Steinig
, Lachlan J. M. Coin:
Nanoq: ultra-fast quality control for nanopore reads. 2991 - Jack L. B. Line:
'WODEN': A CUDA-enabled package to simulate low-frequency radio interferometric data. 3676 - Stephanie Frank Singer, Eric M. Tsai:
electiondata: a Python package for consolidating, checking, analyzing, visualizing and exporting election results. 3739 - Thejasvi Beleyur:
"beamshapes": a Python package to generate directivity patterns for various sound source models. 3740 - Benoît Pasquier, François W. Primeau, Seth G. John:
AIBECS.jl: A tool for exploring global marine biogeochemical cycles. 3814 - Nicolas Legrand, Micah Allen:
Systole: A python package for cardiac signal synchrony and analysis. 3832 - Sebastian M. Stammler, Tilman Birnstiel:
Simframe: A Python Framework for Scientific Simulations. 3882 - Nima S. Hejazi, Kara E. Rudolph, Iván Díaz:
'medoutcon': Nonparametric efficient causal mediation analysis with machine learning in 'R'. 3979 - Pascal T. Merz, Wei-Tse Hsu, Matt W. Thompson, Simon Boothroyd, Chris C. Walker, Michael R. Shirts:
physical_validation: A Python package to assess the physical validity of molecular simulation results. 3981 - Thomas Weiß, Tonio Fincke:
SenSARP: A pipeline to pre-process Sentinel-1 SLC data by using ESA SNAP Sentinel-1 Toolbox. 3337 - Tomaz Bregar, Ahmed Mahmoudi, Miha Kodric, Domen Ocepek, Francesco Trainotti, Miha Pogacar, Mert Göldeli, Gregor Cepon, Miha Boltezar, Daniel Rixen:
pyFBS: A Python package for Frequency Based Substructuring. 3399 - William Savran, Maximilian Werner, Danijel Schorlemmer, Philip Maechling:
pyCSEP: A Python Toolkit For Earthquake Forecast Developers. 3658 - Ajay Khanna, David E. Larson, Srivatsan Sridhar, Matthew Mosior, Travis E. Abbott, Susanna Kiwala, Timothy J. Ley, Eric J. Duncavage, Matthew J. Walter, Jason R. Walker, Obi L. Griffith, Malachi Griffith, Christopher A. Miller:
Bam-readcount - rapid generation of basepair-resolution sequence metrics. 3722 - Thibault Roch, Fabian Barras, Philippe H. Geubelle, Jean-François Molinari:
cRacklet: a spectral boundary integral method library for interfacial rupture simulation. 3724 - B. Lungsi Sharma:
diman: A Clojure Package for Dimensional Analysis. 3735 - Jason J. Gellis, Camila Rangel Smith, Robert A. Foley:
PyLithics: A Python package for stone tool analysis. 3738 - Jon Sampedro, Zarrar Khan, Chris R. Vernon, Steven J. Smith, Stephanie Waldhoff, Rita Van Dingenen:
rfasst: An R tool to estimate air pollution impacts on health and agriculture. 3820 - Team Compas, Jeff Riley, Poojan Agrawal, Jim W. Barrett, Kristian Boyett, Floor Broekgaarden, Debatri Chattopadhyay, Sebastian M. Gaebel, Fabian Gittins, Ryosuke Hirai, George Howitt, Stephen Justham, Lokesh Khandelwal, Floris Kummer, Mike Lau, Ilya Mandel, Selma de Mink, Coenraad J. Neijssel, Tim Riley, Lieke van Son, Simon Stevenson, Alejandro Vigna-Gómez, Serena Vinciguerra, Tom Wagg, Reinhold Willcox:
COMPAS: A rapid binary population synthesis suite. 3838 - Perry de Valpine, Sally Paganin, Daniel Turek:
compareMCMCs: An R package for studying MCMC efficiency. 3844 - James Duncan, Rush Kapoor, Abhineet Agarwal, Chandan Singh, Bin Yu:
VeridicalFlow: a Python package for building trustworthy data science pipelines with PCS. 3895 - Arundale Ramanathan:
Unishox: A hybrid encoder for Short Unicode Strings. 3919 - Zeng Liew, Shozen Dan, Naoki Saito:
WaveletsExt.jl: Extending the boundaries of wavelets in Julia. 3937 - Michael Hall:
Rasusa: Randomly subsample sequencing reads to a specified coverage. 3941 - Justin Shenk, Mats L. Richter, Wolf Byttner:
Delve: Neural Network Feature Variance Analysis. 3992 - Alan A. Kaptanoglu, Brian de Silva, Urban Fasel, Kadierdan Kaheman, Andy Goldschmidt, Jared Callaham, Charles B. Delahunt, Zachary Nicolaou, Kathleen P. Champion, Jean-Christophe Loiseau, J. Nathan Kutz, Steven L. Brunton:
PySINDy: A comprehensive Python package for robust sparse system identification. 3994 - Youjiao Yu:
mixR: An R package for Finite Mixture Modeling for Both Raw and Binned Data. 4031 - Michael J. Mahoney, Colin M. Beier, Aidan Ackerman:
terrainr: An R package for creating immersive virtual environments. 4060 - Aaron Bray, Rachel B. Clipp, M. Umar Qureshi, Sorin Mitran, Andinet Enquobahrie:
gLBM: A GPU enabled Lattice Boltzmann Method Library. 2555 - Szymon Molinski:
Pyinterpolate: Spatial interpolation in Python for point measurements and aggregated datasets. 2869 - Eric Winter, Robert Weigel:
'nnde': A Python package for solving differential equations using neural networks. 3465 - Nicholas Gorman, Anna Bruce, Iain MacGill:
Nempy: A Python package for modelling the Australian National Electricity Market dispatch procedure. 3596 - Samuel Duffield:
bmm: Bayesian Map-matching. 3651 - John Brennan, Lee J. O'Riordan, Kenneth Hanley, Myles Doyle, Momme Allalen, David Brayford, Luigi Iapichino, Niall Moran:
QXTools: A Julia framework for distributed quantum circuit simulation. 3711 - Marten Koopmans, Vincent M. Le Corre, L. Jan Anton Koster:
'SIMsalabim': An open-source drift-diffusion simulator for semiconductor devices. 3727 - Vishwas Rao, Charlotte A. L. Haley, Mihai Anitescu:
LaplaceInterpolation.jl: A Julia package for fast interpolation on a grid. 3766 - Larkin Liu, Jun Tao Luo:
mctreesearch4j: A Monte Carlo Tree Search Implementation for the JVM. 3804 - Christopher Cave-Ayland, Michael J. Bearpark, Charles Romain, Henry S. Rzepa:
CHAMP is a HPC Access and Metadata Portal. 3824 - Ronny Bergmann:
Manopt.jl: Optimization on Manifolds in Julia. 3866 - Alexander Rockhill, Eric Larson, Brittany Stedelin, Alessandra Mantovani, Ahmed M. Raslan, Alexandre Gramfort, Nicole C. Swann:
Intracranial Electrode Location and Analysis in MNE-Python. 3897 - Juan E. Sanchez:
DEVSIM: A TCAD Semiconductor Device Simulator. 3898 - Alexander Pastukhov:
bistablehistory: an R package for history-dependent analysis of perceptual time series. 3901 - Christopher J. Woods, Lester O. Hedges, Christopher Edsall, Ellen Brooks-Pollock, Christopher Parton-Fenton, Trevelyan J. McKinley, Matt J. Keeling, Leon Danon:
MetaWards: A flexible metapopulation framework for modelling disease spread. 3914 - Guillaume Sagnol, Maximilian Stahlberg:
PICOS: A Python interface to conic optimization solvers. 3915 - Nora Loose, Ryan Abernathey, Ian G. Grooms, Julius Busecke, Arthur Guillaumin, Elizabeth Yankovsky, Gustavo Marques, Jacob Steinberg, Andrew Slavin Ross, Hemant Khatri, Scott Bachman, Laure Zanna, Paige Martin:
GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data. 3947 - Bram van Dijk:
Cacatoo: building, exploring, and sharing spatially structured models of biological systems. 3948 - Dominique Sydow, Jaime Rodríguez-Guerra, Andrea Volkamer:
OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database. 3951 - Tangi Migot, Dominique Orban, Abel Soares Siqueira:
DCISolver.jl: A Julia Solver for Nonlinear Optimization using Dynamic Control of Infeasibility. 3991 - Anthony Villano, Kitty Harris, Staci Brown:
'nrCascadeSim' - A simulation tool for nuclear recoil cascades resulting from neutron capture. 3993 - Tom Wagg, Katelyn Breivik, Selma de Mink:
LEGWORK: A python package for computing the evolution and detectability of stellar-origin gravitational-wave sources with space-based detectors. 3998 - Thomas G. Tranter, Robert Timms, Valentin Sulzer, Ferran Brosa Planella, Gavin M. Wiggins, Suryanarayana Vikrant Karra, Priyanshu Agarwal, Saransh Chopra, Srikanth Allu, Paul R. Shearing, Dan J. L. Brett:
liionpack: A Python package for simulating packs of batteries with PyBaMM. 4051 - Rafael Henkin, Michael R. Barnes:
visxhclust: An R Shiny package for visual exploration of hierarchical clustering. 4074 - Nicki Skafte Detlefsen, Jirí Borovec, Justus Schock, Ananya Harsh Jha, Teddy Koker, Luca Di Liello, Daniel Stancl, Changsheng Quan, Maxim Grechkin, William Falcon:
TorchMetrics - Measuring Reproducibility in PyTorch. 4101
Volume 7, Number 71, March 2022
- Alex Malins, Thom Lemoine:
radioactivedecay: A Python package for radioactive decay calculations. 3318 - Eric W. H. Hutton, Mark D. Piper, Gregory E. Tucker:
The Babelizer: language interoperability for model coupling in the geosciences. 3344 - Richard A. Erickson, Daniel S. Stich, Jillian L. Hebert:
fishStan: Hierarchical Bayesian models for fisheries. 3444 - Noah Pflugradt, Peter Stenzel, Leander Kotzur, Detlef Stolten:
LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles. 3574 - Dan E. Kelley, Clark Richards, Chantelle Layton:
oce: an R package for Oceanographic Analysis. 3594 - Milan S. Roberson, Christoffer Fremling, Mansi M. Kasliwal:
DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data. 3612 - Arkajyoti Saha, Sumanta Basu, Abhirup Datta:
RandomForestsGLS: An R package for Random Forests for dependent data. 3780 - Maria Politi, Abdul Moeez, David Beck, Stuart Adler, Lilo Pozzo:
HARDy: Handling Arbitrary Recognition of Data in Python. 3829 - Boris Shminke:
gym-saturation: an OpenAI Gym environment for saturation provers. 3849 - Margaret C. Siple, André E. Punt, Tessa B. Francis, Philip S. Hammond, Dennis Heinemann, Kristy J. Long, Jeffrey Moore, Maritza Sepúlveda, Randall R. Reeves, Guðjón Már Sigurðsson, Gísli Víkingsson, Paul R. Wade, Rob Williams, Alexandre N. Zerbini:
mmrefpoints: Projecting long-term marine mammal abundance with bycatch. 3888 - Frederik De Ceuster, Thomas Ceulemans, Atulit Srivastava, Ward Homan, Jan Bolte, Jeremy Yates, Leen Decin, Peter Boyle, James Hetherington:
3D Line Radiative Transfer & Synthetic Observations with Magritte. 3905 - David E. Graff, Connor W. Coley:
pyscreener: A Python Wrapper for Computational Docking Software. 3950 - Thomas A. r. Purcell, Matthias Scheffler, Christian Carbogno, Luca M. Ghiringhelli:
SISSO++: A C++ Implementation of the Sure-Independence Screening and Sparsifying Operator Approach. 3960 - Matthieu Aussal, Marc Bakry, Laurent Séries:
Castor: A C++ library to code "à la Matlab". 3965 - Jan Baumgärtner, Torben Miller:
TriP: A Python package for the kinematic modeling of serial-parallel hybrid robots. 3967 - Sindre Nordmark Olufsen, Rene Kaufmann, Egil Fagerholt, Vegard Aune:
RECOLO: A Python package for the reconstruction of surface pressure loads from kinematic fields using the virtual fields method. 3980 - Joe Wandy, Vinny Davies, Ross McBride, Stefan Weidt, Simon Rogers, Rónán Daly:
ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. 3990 - Joshua Tse, Marco Molinari, Stephen C. Parker, Adam Symington:
SurfinPy 2.0: A Phase Diagram Generator for Surfaces and Bulk Phases. 4014 - Björn Biltzinger, J. Michael Burgess, Thomas Siegert:
PySPI: A python analysis framework for INTEGRAL/SPI. 4017 - Qing Yu, Jian Yuan:
TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization. 4021 - Charles Li:
helayo: Reconstructing Sanskrit texts from manuscript witnesses. 4022 - Houman Mirzaalian-Dastjerdi, Reza Gholami Mahmoodabadi, Matthias Bär, Vahid Sandoghdar, Harald Köstler:
PiSCAT: A Python Package for Interferometric Scattering Microscopy. 4024 - Rick Helmus, Bas van de Velde, Andrea M. Brunner, Thomas L. ter Laak, Annemarie P. van Wezel, Emma Schymanski:
patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening. 4029 - Jeffrey W. Hollister, Dorothy Q. Kellogg, Qian Lei-Parent, Emily Wilson, Cary Chadwick, David Dickson, Arthur Gold, Chester Arnold:
nsink: An R package for flow path nitrogen removal estimation. 4039 - Nastaran Saffaryazdi, Aidin Gharibnavaz, Mark Billinghurst:
Octopus Sensing: A Python library for human behavior studies. 4045 - Frederik Kratzert, Martin Gauch, Grey Nearing, Daniel Klotz:
NeuralHydrology - A Python library for Deep Learning research in hydrology. 4050 - Daniel Dee, Dean Corriveau, Jeffrey R. Ladd, Lakshmi Nannapaneni, John Arkins, Jeffrey Brown:
PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks. 4062 - Victor Sacek, Jamison Assunção, Agustina Pesce, Rafael Monteiro da Silva:
Mandyoc: A finite element code to simulate thermochemical convection in parallel. 4070 - Jiahe Cui, Karen M. Hampson, Matthew Wincott, Martin J. Booth:
SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software. 4075 - Floris van Breugel, Yuying Liu, Bingni W. Brunton, J. Nathan Kutz:
PyNumDiff: A Python package for numerical differentiation of noisy time-series data. 4078 - Aliaksei Pilko, Zachary Tait:
SEEDPOD Ground Risk: A Python application and library for Uncrewed Aerial Systems ground risk analysis and risk-aware path finding. 4079 - Alphons Gwatimba, Joseph Ho, Thomas Iosifidis, Yuliya V. Karpievitch:
Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow. 4080 - Brandon Silva, Paul Lunis, Marios Theristis, Hubert Seigneur:
PyPVRPM: Photovoltaic Reliability and Performance Model in Python. 4093 - Leonid P. Pryadko, Vadim A. Shabashov, Valerii K. Kozin:
QDistRnd: A GAP package for computing the distance of quantum error-correcting codes. 4120 - Paul Stocker:
'NGSTrefftz': Add-on to NGSolve for Trefftz methods. 4135 - Benjamin M. Gyori, Charles Tapley Hoyt:
PyBioPAX: biological pathway exchange in Python. 4136 - Aaron R. Caldwell:
SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses. 4148 - Coleman R. Harris, Julia Wrobel, Simon N. Vandekar:
mxnorm: An R Package to Normalize Multiplexed Imaging Data. 4180
Volume 7, Number 72, April 2022
- Grant Giesbrecht, Ariel Amsellem, Timo Bauer, Brian Mak, Brian Wynne, Zhihao Qin, Arun Persaud:
Hardware-Control: Instrument control and automation package. 2688 - Jorge Dávila-Chacón, Max Pumperla:
Logodetect: One-shot detection of logos in image and video data. 3124 - Piotr Bartman, Oleksii Bulenok, Kamil Górski, Anna Jaruga, Grzegorz Lazarski, Michael A. Olesik, Bartosz Piasecki, Clare E. Singer, Aleksandra Talar, Sylwester Arabas:
PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry. 3219 - Juniper Simonis, Glenda Yenni, Ellen Bledsoe, Erica Christensen, Henry Senyondo, Shawn D. Taylor, Hao Ye, Ethan P. White, S. K. Morgan Ernest:
portalcasting: Supporting automated forecasting of rodent populations. 3220 - Dustin S. Stoltz, Marshall A. Taylor:
text2map: R Tools for Text Matrices. 3741 - Simon Dobson:
epyc: Computational experiment management in Python. 3764 - Joshua D. Larsen, Ayman H. Alzraiee, Richard G. Niswonger:
Integrated hydrologic model development and postprocessing for GSFLOW using pyGSFLOW. 3852 - Fabian Wüllhorst, Thomas Storek, Philipp Mehrfeld, Dirk Müller:
AixCaliBuHA: Automated calibration of building and HVAC systems. 3861 - Mithun Bairagi:
GiNaCDE: the high-performance F-expansion and First Integral Methods with C++ library for solving Nonlinear Differential Equations. 3885 - Nicholas M. Anthony, Vadim Backman:
PWSpy: A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data. 3957 - Fredrik Strömberg:
hilbertmodgroup: Reduction algorithms and framework for Hilbert Modular Groups. 3996 - Francesco Nattino, Ou Ku, Meiert W. Grootes, Emma Izquierdo-Verdiguier, Serkan Girgin, Raúl Zurita-Milla:
CGC: a Scalable Python Package for Co- and Tri-Clustering of Geodata Cubes. 4032 - Chung-hong Chan:
sweater: Speedy Word Embedding Association Test and Extras Using R. 4036 - Andrea M. Whittaker:
ADaPT-ML: A Data Programming Template for Machine Learning. 4038 - Sigurd M. Albrektsen, Kasper Gade Bøtker Rasmussen, Anders E. Liverud, Steffen Dalgard, Jakob Høgenes, Silje Ekroll Jahren, Jan Kocbach, Trine M. Seeberg:
The AutoActive Research Environment. 4061 - Jeremie Coullon, Christopher Nemeth:
SGMCMCJax: a lightweight JAX library for stochastic gradient Markov chain Monte Carlo algorithms. 4113 - Stuart R. Slattery, Samuel Temple Reeve, Christoph Junghans, Damien Lebrun-Grandié, Robert F. Bird, Guangye Chen, Shane Fogerty, Yuxing Qiu, Stephan Schulz, Aaron Scheinberg, Austin Isner, Kwitae Chong, Stan G. Moore, Timothy C. Germann, James F. Belak, Susan M. Mniszewski:
Cabana: A Performance Portable Library for Particle-Based Simulations. 4115 - Gereon A. Kaiping, Melvin S. Steiger, Natalia Chousou-Polydouri:
Lexedata: A toolbox to edit CLDF lexical datasets. 4140 - Nathan Bell, Luke N. Olson, Jacob B. Schroder:
PyAMG: Algebraic Multigrid Solvers in Python. 4142 - Tsung-Lin Wu, Amr Alhossary, Todd C. Pataky, Wei Tech Ang, Cyril J. Donnelly:
pyemgpipeline: A Python package for electromyography processing. 4156 - Bardhyl Miftari, Mathias Berger, Hatim Djelassi, Damien Ernst:
GBOML: Graph-Based Optimization Modeling Language. 4158 - Michal M. Wieclaw:
tesliper: a theoretical spectroscopist's little helper. 4164 - Peter Kraus, Nicolas Vetsch, Corsin Battaglia:
yadg: yet another datagram. 4166 - Elizabeth Newman, Lars Ruthotto:
'hessQuik': Fast Hessian computation of composite functions. 4171 - Roi Kugel, Josh Borrow:
swift-emulator: A Python package for emulation of simulated scaling relations. 4240 - Martin Larralde:
Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. 4296 - Stefan Jaud, Helge Hecht, Jonas Schlenger, Julian Amann:
TUM Open Infra Platform: an open source package for simultaneous viewing and analysis of digital models in the civil engineering domain. 3061
Volume 7, Number 73, May 2022
- Sasha Petrenko, Donald C. Wunsch:
AdaptiveResonance.jl: A Julia Implementation of Adaptive Resonance Theory (ART) Algorithms. 3671 - Alexander Jüstel, Arthur Endlein Correira, Marius Pischke, Miguel de la Varga, Jan Florian Wellmann:
GemGIS - Spatial Data Processing for Geomodeling. 3709 - Elizabeth Julia Monte, Alexandru Andrei Vasile, James Lowman, Nasser Mohieddin Abukhdeir:
OpenCMP: An Open-Source Computational Multiphysics Package. 3742 - Véronique Legrand, Thomas Kergrohen, Nicolas Joly, Alexis Criscuolo:
ROCK: digital normalization of whole genome sequencing data. 3790 - Jonas Lamy, Thibault Pelletier, Guillaume Lienemann, Benoît Magnin, Bertrand Kerautret, Nicolas Passat, Julien Finet, Antoine Vacavant:
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images. 3920 - Nicolas Galtier, Claire Guerrier:
Sinaps: A Python library to simulate voltage dynamics and ionic electrodiffusion in neurons. 4012 - Alexander Bauer, Maximilian Weigert, Hawre Jalal:
APCtools: Descriptive and Model-based Age-Period-Cohort Analysis. 4056 - Conor Heins, Beren Millidge, Daphne Demekas, Brennan Klein, Karl J. Friston, Iain D. Couzin, Alexander Tschantz:
pymdp: A Python library for active inference in discrete state spaces. 4098 - Lily Wang, Megan L. O'Mara:
PsiRESP: calculating RESP charges with Psi4. 4100 - Mick Carter, David Blunck:
pypbomb: A Python package with tools for the design of detonation tubes. 4143 - Marcin Wojdyr:
GEMMI: A library for structural biology. 4200 - Zhen Wu, Gael Forget:
PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model. 4207 - Al-Ahmadgaid B. Asaad, Arnold R. Salvacion, Bui Tan Yen:
ALUES: R package for Agricultural Land Use Evaluation System. 4228 - Anders Granholm, Aksel Karl Georg Jensen, Theis Lange, Benjamin Skov Kaas-Hansen:
adaptr: an R package for simulating and comparing adaptive clinical trials. 4284 - Michael Gully-Santiago, Jessica L. Luna, Caroline V. Morley, Kyle Kaplan, Aishwarya Ganesh, Erica A. Sawczynec, Joel Burke, Daniel M. Krolikowski:
Astronomical échelle spectroscopy data analysis with 'muler'. 4302 - Roman Parise, Georgios Is. Detorakis:
OpenPelt: Python Framework for Thermoelectric Temperature Control System Development. 4306 - Michael J. Mahoney, Colin M. Beier, Aidan Ackerman:
unifir: A Unifying API for Working with Unity in R. 4388 - Gustave Coste, Arnaud Hélias:
PEFAP : Estimating the environmental footprint of food products from packaging data. 3329
Volume 7, Number 74, June 2022
- Xin Feng, Germano Barcelos, James D. Gaboardi, Elijah Knaap, Ran Wei, Levi John Wolf, Qunshan Zhao, Sergio J. Rey:
spopt: a python package for solving spatial optimization problems in PySAL. 3330 - Felix Wiebe, Jonathan Babel, Shivesh Kumar, Shubham Vyas, Daniel Harnack, Melya Boukheddimi, Mihaela Popescu, Frank Kirchner:
Torque-limited simple pendulum: A toolkit for getting familiar with control algorithms in underactuated robotics. 3884 - Samuel Burbulla, Andreas Dedner, Maximilian Hörl, Christian Rohde:
Dune-MMesh: The Dune Grid Module for Moving Interfaces. 3959 - Matthew W. Scroggs, Igor A. Baratta, Chris N. Richardson, Garth N. Wells:
Basix: a runtime finite element basis evaluation library. 3982 - Taylor McDonnell, Andrew Ning:
GXBeam: A Pure Julia Implementation of Geometrically Exact Beam Theory. 3997 - Evgeny Moerman, Felix Hummel, Andreas Grüneis, Andreas Irmler, Matthias Scheffler:
Interface to high-performance periodic coupled-cluster theory calculations with atom-centered, localized basis functions. 4040 - Lucas Timotheo Sanches:
'QuasinormalModes.jl': A Julia package for computing discrete eigenvalues of second order ODEs. 4077 - Yasin Maan Yousif, Awad Mukbil, Jörg P. Müller:
OfflineMOT: A Python package for multiple objects detection and tracking from bird view stationary drone videos. 4099 - Erling Andersen:
Imagedata: A Python library to handle medical image data in NumPy array subclass Series. 4133 - Santiago Badia, Alberto F. Martín, Francesc Verdugo:
GridapDistributed: a massively parallel finite element toolbox in Julia. 4157 - Michael Kilgour, Tao Liu, Ilya S. Dementyev, Lena Simine:
E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands. 4182 - Matthew Pitkin:
lintegrate: A C/Python numerical integration library for working in log-space. 4231 - Antun Skuric, Hasan Sinan Bank, Richard Unger, Owen Williams, David González-Reyes:
SimpleFOC: A Field Oriented Control (FOC) Library for Controlling Brushless Direct Current (BLDC) and Stepper Motors. 4232 - Jon Schwenk, Tal Zussman, Jemma Stachelek, Joel C. Rowland:
rabpro: global watershed boundaries, river elevation profiles, and catchment statistics. 4237 - Cristiane Hayumi Taniguti, Gabriel Siqueira de Gesteira, Jeekin Lau, Guilherme Silva da Pereira, Zhao-Bang Zeng, David Byrne, Oscar Riera-Lizarazu, Marcelo Mollinari:
VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. 4242 - Patrick Reichherzer, Julia K. Becker Tjus:
PropPy - Correlated random walk propagation of cosmic rays in magnetic turbulence. 4243 - Sébastien Tourbier, Joan Rué Queralt, Katharina Glomb, Yasser Alemán-Gómez, Emeline Mullier, Alessandra Griffa, Mikkel Schöttner, Jonathan Wirsich, Mustafa Anil Tuncel, Jakub Jancovic, Meritxell Bach Cuadra, Patric Hagmann:
Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping. 4248 - Craig Gower-Page, Alessandro Noci, Marcel Wolbers:
rbmi: A R package for standard and reference-based multiple imputation methods. 4251 - Gabriele Lubatti, Elmir Mahammadov, Antonio Scialdone:
MitoHEAR: an R package for the estimation and downstream statistical analysis of the mitochondrial DNA heteroplasmy calculated from single-cell datasets. 4265 - Aurore Loisy, Christophe Eloy:
OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP. 4266 - George Yiasemis, Nikita Moriakov, Dimitrios Karkalousos, Matthan W. A. Caan, Jonas Teuwen:
DIRECT: Deep Image REConstruction Toolkit. 4278 - Dana Solav, Asaf Silverstein:
DuoDIC: 3D Digital Image Correlation in MATLAB. 4279 - Christopher L. Aberson:
BetterReg: An R package for Useful Regression Statistics. 4280 - Mojtaba Barzegari, Liesbet Geris:
BioDeg: A finite element software for the simulation of the corrosion and biodegradation process in metallic biomaterials. 4281 - Sarah Zwiep, Shawn M. Chartrand:
pySBeLT: A Python software package for stochastic sediment transport under rarefied conditions. 4282 - Maximilian Bittens:
VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data. 4300 - Yannik Schälte, Emmanuel Klinger, Emad Alamoudi, Jan Hasenauer:
pyABC: Efficient and robust easy-to-use approximate Bayesian computation. 4304 - Vipin Agrawal, Vikash Pandey, Hanna Kylhammar, Apurba Dev, Dhrubaditya Mitra:
MeMC: A package for Monte Carlo simulations of spherical shells. 4305 - Kendall L. Mongird, Konstantinos Oikonomou, Juliet S. Homer, Jennie S. Rice:
interflow: A Python package to organize, calculate, and visualize sectoral interdependency flow data. 4336 - Arne Küderle, Nils Roth, Robert Richer, Bjoern M. Eskofier:
imucal - A Python library to calibrate 6 DOF IMUs. 4338 - Warrick Ball:
tomso: TOols for Models of Stars and their Oscillations. 4343 - Anja Weigel, Fadoua Balabdaoui, Yulia Kulagina, Lilian Mueller:
mixComp: An R package for estimating complexity of a mixture. 4354 - Maxime Borry, Alexander Hübner, Christina Warinner:
sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files. 4360 - Mattis Magg, Tilman Hartwig, Li-Hsin Chen, Yuta Tarumi:
A-SLOTH: Ancient Stars and Local Observables by Tracing Halos. 4417 - Alessandro Santuz:
musclesyneRgies: factorization of electromyographic data in R with sensible defaults. 4439 - Edward W. J. Wallace, Samuel J. Haynes:
tidyqpcr: Quantitative PCR analysis in the tidyverse. 4507
Volume 7, Number 75, July 2022
- Shuo Ma, Muhao Chen, Robert E. Skelton:
TsgFEM: Tensegrity Finite Element Method. 3390 - Alexander Moriarty, Kazuki Morita, Keith T. Butler, Aron Walsh:
UnlockNN: Uncertainty quantification for neural network models of chemical systems. 3700 - Frédéric J. P. Richard:
PyAFBF: a Python library for sampling image textures from the anisotropic fractional Brownian field. 3821 - Enrico Ferrea, Pierre Morel, Alexander Gail:
BCImat: a Matlab-based framework for Intracortical Brain-Computer Interfaces and their simulation with an artificial spiking neural network. 3956 - Tiago F. Sequeira:
NeuralFieldEq.jl: A flexible solver to compute Neural Field Equations in several scenarios. 3974 - Asher Pembroke, Darren De Zeeuw, Lutz Rastaetter, Rebecca Ringuette, Oliver Gerland, Dhruv Patel, Michael T. Contreras:
Kamodo: A functional API for space weather models and data. 4053 - Azadeh Moradinezhad Dizgah, Alberto Vallinotto, Farnik Nikakhtar:
limHaloPT: A Numerical Package for Accurate Modeling of Line Intensity Power Spectrum. 4173 - Erich Schubert, Lars Lenssen:
Fast k-medoids Clustering in Rust and Python. 4183 - Benjamin Kurt Miller, Alex Cole, Christoph Weniger, Francesco Nattino, Ou Ku, Meiert W. Grootes:
swyft: Truncated Marginal Neural Ratio Estimation in Python. 4205 - Robert Turnbull, Jonathan Garber:
ausdex: A Python package for adjusting Australian dollars for inflation. 4212 - Konrad Kollnig, Nigel Shadbolt:
TrackerControl: Transparency and Choice around App Tracking. 4270 - Mario Krattenmacher, Markus Müller, Pascal Kuthe, Michael Schröter:
DMT-core: A Python Toolkit for Semiconductor Device Engineers. 4298 - Benjamin W. L. Margolis, Kenneth R. Lyons:
SimuPy Flight Vehicle Toolkit. 4299 - Marc Costa Sitja:
NAIF PDS4 Bundler: A Python package to generate SPICE PDS4 archives. 4327 - Sébastien Plutniak:
Archeofrag: an R package for Refitting and Spatial Analysis in Archaeology. 4335 - Helge Hecht, Maksym Skoryk, Martin Cech, Elliott James Price:
RIAssigner: A package for gas chromatographic retention index calculation. 4337 - Jack D. Sundberg, Siona S. Benjamin, Lauren M. McRae, Scott Warren:
Simmate: a framework for materials science. 4364 - Jonah M. Miller, Daniel Holladay, Chad D. Meyer, Joshua C. Dolence, Sriram Swaminarayan, Christopher M. Mauney, Karen Tsai:
Spiner: Performance Portable Routines for Generic, Tabulated, Multi-Dimensional Data. 4367 - Magnus G. Jespersen, Andrew Hayes, Mark R. Davies:
Magphi: Sequence extraction tool from FASTA and GFF3 files using seed pairs. 4369 - Diederik Coppitters, Panagiotis Tsirikoglou, Ward De Paepe, Konstantinos Kyprianidis, Anestis Kalfas, Francesco Contino:
RHEIA: Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems. 4370 - Dominic Chmiel, Samuel Wallan, Matt Haberland:
'tukey_hsd': An Accurate Implementation of the Tukey Honestly Significant Difference Test in Python. 4383 - Ron Shnapp:
MyPTV: A Python Package for 3D Particle Tracking. 4398 - Denis Brizard:
elwaspatid: A Python package to compute space-time diagrams for the propagation of elastic waves in 1D rods. 4418 - Eric Sadit Tellez, Guillermo Ruiz:
'SimilaritySearch.jl': Autotuned nearest neighbor indexes for Julia. 4442 - Ayush Garg, Richard Smith-Unna, Peter Murray-Rust:
'pygetpapers': a Python library for automated retrieval of scientific literature. 4451 - Thomas Pinder, Daniel Dodd:
GPJax: A Gaussian Process Framework in JAX. 4455 - Juanjo Bazán, Mercedes Mollá:
Starmatrix: Modelling nucleosynthesis of galactic chemical elements. 4461 - Simon Couch, Max Kuhn:
stacks: Stacked Ensemble Modeling with Tidy Data Principles. 4471 - Dillon Bowen:
Multiple Inference: A Python package for comparing multiple parameters. 4492 - Johannes Fett, Urs Kober, Christian Schwarz, Dirk Habich, Wolfgang Lehner:
Accelerating Parallel Operation for Compacting Selected Elements on GPUs. 4589
Volume 7, Number 76, August 2022
- Candace Makeda Moore, Andrew Murphy, Oleg Sivokon, Patrice J. Musoke:
CleanX: A Python library for data cleaning of large sets of radiology images. 3632 - Egor Orachev, Maria Karpenko, Pavel Alimov, Semyon V. Grigorev:
SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations. 3743 - Martin H. Skjelvareid:
Synaptus: A Matlab/Octave toolbox for synthetic aperture ultrasound imaging. 4185 - Andrew P. Valentine, Malcolm Sambridge:
pyprop8: A lightweight code to simulate seismic observables in a layered half-space. 4217
Volume 7, Number 77, September 2022
- Stefan Zitz, Manuel Zellhöfer, Andrea Scagliarini, Jens Harting:
Swalbe.jl: A lattice Boltzmann solver for thin film hydrodynamics. 4312 - Daniel E. Kaufman, Sha Feng, Katherine V. Calvin, Bryce E. Harrop, Susannah Burrows:
gdess: A framework for evaluating simulated atmospheric CO~2~ in Earth System Models. 4326 - Jeryn Chang, Frederik Steyn, Shyuan Ngo, Robert Henderson, Christine Cong Guo, Steffen Bollmann, Jurgen Fripp, Markus Barth, Thomas B. Shaw:
Open-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7T. 4368 - Ejike Ugba:
gofcat: An R package for goodness-of-fit of categorical response models. 4382 - J. W. Ngan, Colin C. Caprani:
'ospgrillage': A bridge deck grillage analysis preprocessor for 'OpenSeesPy'. 4404 - Wouter Peere, Tobias Blanke:
GHEtool: An open-source tool for borefield sizing in Python. 4406 - Michal Burdukiewicz, Andrej-Nikolai Spiess, Dominik Rafacz, Konstantin Blagodatskikh, Stefan Rödiger:
PCRedux: A Quantitative PCR Machine Learning Toolkit. 4407 - Adam J. Fleischhacker, Thi Hong Nhung Nguyen:
Generative DAGs as an Interface Into Probabilistic Programming with the R Package causact. 4415 - Matthias Demuzere, Daniel Argüeso, Andrea Zonato, Jonas Kittner:
W2W: A Python package that injects WUDAPT's Local Climate Zone information in WRF. 4432 - Jakob McBroome, Yatish Turakhia, Russell Corbett-Detig:
BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees. 4433 - Tamás Gál, Jerry (Jiahong) Ling, Nick Amin:
UnROOT: an I/O library for the CERN ROOT file format written in Julia. 4452 - Paul Tiede:
Comrade: Composable Modeling of Radio Emission. 4457 - Vanessa V. Sochat:
CiteLang: Modeling the Research Software Ecosystem. 4458 - Karla Cervantes Barron, Jonathan M. Cullen:
Mat-dp: An open-source Python model for analysing material demand projections and their environmental implications, which result from building low-carbon systems. 4460 - Ítalo Epifânio, Oleksandr Pysarenko, Immanuel Bayer:
Ipyannotator: the infinitely hackable annotation framework. 4480 - Adam Li, Jacob Feitelberg, Anand Prakash Saini, Richard Höchenberger, Mathieu Scheltienne:
MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python. 4484 - Tomás E. Müller-Bravo, Lluís Galbany:
HostPhot: global and local photometry of galaxies hosting supernovae or other transients. 4508 - Sterling G. Baird, Kevin Maik Jablonka, Michael D. Alverson, Hasan M. Sayeed, Mohammed Faris Khan, Colton Seegmiller, Berend Smit, Taylor D. Sparks:
xtal2png: A Python package for representing crystal structure as PNG files. 4528 - Brandon Monier, Terry M. Casstevens, Peter J. Bradbury, Edward S. Buckler:
rTASSEL: An R interface to TASSEL for analyzing genomic diversity. 4530 - Travis L. Seymour:
EPICpy: A Python Interface for EPIC Computational Cognitive Modeling. 4533 - Max A. Little:
GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference. 4534 - Tony E. Wong, Lisa Rennels, Frank Errickson, Vivek Srikrishnan, Alexander Bakker, Klaus Keller, David Anthoff:
MimiBRICK.jl: A Julia package for the BRICK model for sea-level change in the Mimi integrated modeling framework. 4556 - Vaibhav Dixit, Christopher Rackauckas:
GlobalSensitivity.jl: Performant and Parallel Global Sensitivity Analysis with Julia. 4561 - Jan Leppert:
GasChromatographySimulator.jl. 4565 - Dominik Raabe, Henrik Biermann, Manuel Bassek, Martin Wohlan, Rumena Komitova, Robert Rein, Tobias Kuppens Groot, Daniel Memmert:
floodlight - A high-level, data-driven sports analytics framework. 4588 - Alister Johnson, Camille Coti, Allen D. Malony, Johannes Doerfert:
MARTINI: The Little Match and Replace Tool for Automatic Code Rewriting. 4590 - Peter Sanders, Dominik Schreiber:
Mallob: Scalable SAT Solving On Demand With Decentralized Job Scheduling. 4591 - Mustapha Regragui, Baptiste Coye, Laércio Lima Pilla, Raymond Namyst, Denis Barthou:
SimSGamE : Scheduling simulator for modern game engines. 4592 - Siavash Saki, Jonas Hamann, Tobias Hagen:
TessPy: a python package for geographical tessellation. 4620 - Gáspár Lukács:
POSSA: Power simulation for sequential analyses and multiple hypotheses. 4643 - Vincent A. Cicirello:
$\rho\mu$: A Java library of randomization enhancements and other math utilities. 4663 - Piotr Bartman, Jakub Banaskiewicz, Szymon Drenda, Maciej Manna, Michael A. Olesik, Pawel Rozwoda, Michal Sadowski, Sylwester Arabas:
PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab. 3896 - Zarrar Khan, Mengqi Zhao, Chris R. Vernon, Thomas Wild, Brinda Yarlagadda:
rmap: An R package to plot and compare tabular data on customizable maps across scenarios and time. 4015 - Kelly A. Douglass, Dahlia Veyrat, Stephen W. O'Neill, Segev Y. BenZvi, Fatima Zaidouni, Michaela Guzzetti:
VAST: the Void Analysis Software Toolkit. 4033 - Nathan Green, Anna Heath, Gianluca Baio:
BCEA: An R Package for Cost-Effectiveness Analysis. 4206 - Sietze Norder, Laura Becker, Hedvig Skirgård, Leonardo Arias, Alena Witzlack-Makarevich, Rik van Gijn:
glottospace: R package for language mapping and geospatial analysis of linguistic and cultural data. 4303 - David Pagnon, Mathieu Domalain, Lionel Revéret:
Pose2Sim: An open-source Python package for multiview markerless kinematics. 4362 - Richard Brearton, Andrew McCluskey, Tim Snow:
islatu: A Python package for the reduction of reflectometry data. 4397 - Kristian Agasøster Haaga, George Datseris:
TimeseriesSurrogates.jl: a Julia package for generating surrogate data. 4414
Volume 7, Number 78, October 2022
- Eva-Maria Grommes, Ulf Blieske:
BifacialSimu: Holistic Simulation of large-scale Bifacial Photovoltaic Systems. 4443 - Ziga Stupan, Iztok Fister Jr.:
NiaARM: A minimalistic framework for Numerical Association Rule Mining. 4448 - Victor H. Chávez, Jonathan Nafziger, Adam Wasserman:
pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations. 4459 - Yijie Xia, Yi Qin Gao:
Xponge: A Python package to perform pre- and post-processing of molecular simulations. 4467 - Lucy D'Agostino McGowan:
tipr: An R package for sensitivity analyses for unmeasured confounders. 4495 - Luis Barroso-Luque, Julia H. Yang, Fengyu Xie, Tina Chen, Ronald L. Kam, Zinab Jadidi, Peichen Zhong, Gerbrand Ceder:
smol: A Python package for cluster expansions and beyond. 4504 - Nima S. Hejazi, Mark J. van der Laan, David C. Benkeser:
'haldensify': Highly adaptive lasso conditional density estimation in 'R'. 4522 - David Schoch:
netrankr: An R package for total, partial, and probabilistic rankings in networks. 4563 - Matthew Pitkin:
CWInPy: A Python package for inference with continuous gravitational-wave signals from pulsars. 4568 - Paul Ortmann, Chris M. J. Tampère:
dyntapy: dynamic and static traffic assignment in Python. 4593 - David Biagioni, Charles Edison Tripp, Struan Clark, Dmitry Duplyakin, Jeffrey N. Law, Peter C. St. John:
graphenv: a Python library for reinforcement learning on graph search spaces. 4621 - Maximilian E. Merkel, Alberto Carta, Sophie Beck, Alexander Hampel:
solid_dmft: gray-boxing DFT+DMFT materials simulations with TRIQS. 4623 - Alexander Riss:
SpmImage Tycoon: Organize and analyze scanning probe microscopy data. 4644 - Branden Butler, Ryan M. Richard:
CMinx: A CMake Documentation Generator. 4680 - Nicholas Brown:
tsp ("Teaspoon"): A library for ground temperature data. 4704 - Byron C. Jaeger, Sawyer Welden, Kristin M. Lenoir, Nicholas M. Pajewski:
aorsf: An R package for supervised learning using the oblique random survival forest. 4705 - Cosima Meyer, Dennis Hammerschmidt:
overviewR - Easily Explore Your Data in R. 4740 - Geoffrey Pruvost, Bilel Derbel, Arnaud Liefooghe:
Moead-framework: a modular MOEA/D Python framework. 2974 - Daniel Eggert, Mike Sips, Philipp S. Sommer, Doris Dransch:
DASF: A data analytics software framework for distributed environments. 4052 - Chi Zhu, Vijay Vedula, David W. Parker, Nathan M. Wilson, Shawn C. Shadden, Alison L. Marsden:
svFSI: A Multiphysics Package for Integrated Cardiac Modeling. 4118 - Théo Matricon, Nathanaël Fijalkow, Guillaume Lagarde, Kevin Ellis:
DeepSynth: Scaling Neural Program Synthesis with Distribution-based Search. 4151 - Joris Vankerschaver, Steven J. Kern, Robert Kern:
VPsearch: fast exact sequence similarity search for genomic sequences. 4236 - Kristina Orehounig, Leonie Fierz, James Allan, Sven Eggimann, Natasa Vulic, Aaron Bojarski:
CESAR-P: A dynamic urban building energy simulation tool. 4261 - Eneko Martin-Martinez, Roger Samsó, James Houghton, Jordi Sole:
PySD: System Dynamics Modeling in Python. 4329 - Jaroslav Fowkes, Lindon Roberts, Árpád Bürmen:
PyCUTEst: an open source Python package of optimization test problems. 4377 - Julian Karl Bauer, Philipp Lothar Kinon, Jonas Hund, Lisa Latussek, Nils Meyer, Thomas Böhlke:
Mechkit: A continuum mechanics toolkit in Python. 4389 - Valentin Christiaens:
special: A Python package for the spectral characterization of directly imaged low-mass companions. 4456 - Stine Fleischer Myhre, Olav Bjarte Fosso, Poul Einar Heegaard, Oddbjørn Gjerde:
RELSAD: A Python package for reliability assessment of modern distribution systems. 4516 - Joren Six:
Panako: a scalable audio search system. 4554 - Simon Biggs, Matthew Jennings, Stuart Swerdloff, Phillip Chlap, Derek Lane, Jacob Rembish, Jacob McAloney, Paul King, Rafael Ayala, Fada Guan, Nicola Lambri, Cody Crewson, Matthew Sobolewski:
PyMedPhys: A community effort to develop an open, Python-based standard library for medical physics applications. 4555 - Victor Férat, Mathieu Scheltienne, Denis Brunet, Tomas Ros, Christoph M. Michel:
Pycrostates: a Python library to study EEG microstates. 4564 - Hagai Rossman, Ayya Keshet, Malka Gorfine:
PyMSM: Python package for Competing Risks and Multi-State models for Survival Data. 4566 - William Becker, Giulio Caperna, Maria Del Sorbo, Hedvig Norlén, Eleni Papadimitriou, Michaela Saisana:
COINr: An R package for developing composite indicators. 4567 - Timothée Giraud:
osrm: Interface Between R and the OpenStreetMap-Based Routing Service OSRM. 4574 - Jeffrey O. Hanson:
wdpar: Interface to the World Database on Protected Areas. 4594 - Clemens Brunner:
MNELAB: a graphical user interface for MNE-Python. 4650 - Stef Smeets, Nicolas Renaud, Lars J. Corbijn van Willenswaard:
Nanomesh: A Python workflow tool for generating meshes from image data. 4654 - Indrajeet Patil, Dominique Makowski, Mattan S. Ben-Shachar, Brenton M. Wiernik, Etienne Bacher, Daniel Lüdecke:
datawizard: An R Package for Easy Data Preparation and Statistical Transformations. 4684 - Oliver N. F. King, Dimitrios Bellos, Mark Basham:
Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep LearningModels. 4691 - Ming Hu, Xiaolong Jiang:
PatchView: A Python Package for Patch-clamp Data Analysis and Visualization. 4706 - Charles Prud'homme, Jean-Guillaume Fages:
Choco-solver: A Java library for constraint programming. 4708 - Bas van Stein, Elena Raponi:
GSAreport: Easy to Use Global Sensitivity Reporting. 4721 - Thilo Balke, Fernando Davis, Cristina Garcia-Cardona, Soumendu Majee, Michael T. McCann, Luke Pfister, Brendt Wohlberg:
Scientific Computational Imaging Code (SCICO). 4722 - Jesús-Adolfo Mejía-de-Dios, Efrén Mezura-Montes:
Metaheuristics: A Julia Package for Single- and Multi-Objective Optimization. 4723 - Rémi Lafage:
egobox, a Rust toolbox for efficient global optimization. 4737
Volume 7, Number 79, November 2022
- Ashley Chontos, Daniel Huber, Maryum Sayeed, Pavadol Yamsiri:
pySYD: Automated measurements of global asteroseismic parameters. 3331 - Christopher R. Wentland, Karthik Duraisamy:
PERFORM: A Python package for developing reduced-order models for reacting fluid flows. 3428 - Kleanthis Natsiopoulos, Nickolaos G. Tzeremes:
ARDL: An R package for the analysis of level relationships. 3496 - Sasha Petrenko, Donald C. Wunsch:
ClusterValidityIndices.jl: Batch and Incremental Metrics for Unsupervised Learning. 3527 - Etienne Combrisson, Ruggero Basanisi, Vinicius Lima Cordeiro, Robin A. A. Ince, Andrea Brovelli:
Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data. 3842 - Matthew Treinish, Ivan Carvalho, Georgios Tsilimigkounakis, Nahum Sá:
rustworkx: A High-Performance Graph Library for Python. 3968 - Colin Grudzien, Charlotte Merchant, Sukhreen Sandhu:
DataAssimilationBenchmarks.jl: a data assimilation research framework. 4129 - Joanna Leng, Jonathan H. Pickering, Sven L. M. Schroeder, Gunjan Das:
CrystalGrowthTracker: A Python package to analyse crystal face advancement rates from time lapse synchrotron radiography. 4333 - Casey R. McGrath, Casey D. Burleyson, Zarrar Khan, Aowabin Rahman, Travis Thurber, Chris R. Vernon, Nathalie Voisin, Jennie S. Rice:
tell: a Python package to model future total electricity loads in the United States. 4472 - Matej Troják, Helge Hecht, Martin Cech, Elliott James Price:
MSMetaEnhancer: A Python package for mass spectra metadata annotation. 4494 - Taylor J. Bell, Eva-Maria Ahrer, Jonathan Brande, Aarynn L. Carter, Adina D. Feinstein, Giannina Guzman Caloca, Megan Mansfield, Sebastian Zieba, Caroline Piaulet, Björn Benneke, Joseph Filippazzo, Erin M. May, Pierre-Alexis Roy, Laura Kreidberg, Kevin B. Stevenson:
Eureka!: An End-to-End Pipeline for JWST Time-Series Observations. 4503 - Patrick Sanan, Dave A. May, Richard Tran Mills, Boris J. P. Kaus:
DMStag: Staggered, Structured Grids for PETSc. 4531 - Muhammad Asad, Reuben Dorent, Tom Vercauteren:
FastGeodis: Fast Generalised Geodesic Distance Transform. 4532 - Thomas Thelen, Marcus Thomson, Gerardo Aldana, Toni Gonzalez:
villager: A framework for designing and executing agent-based models in R. 4562 - Asitha I. Senanayake, Roger J. Chandler, Tony Daly, Edward Lewis:
python-ags4: A Python library to read, write, and validate AGS4 geodata files. 4569 - Tobias Bengfort, Taib Hayat, Timo Göttel:
Castellum: A participant management tool for scientific studies. 4600 - Jeroen G. S. Overschie, Ahmad Alsahaf, George Azzopardi:
fseval: A Benchmarking Framework for Feature Selection and Feature Ranking Algorithms. 4611 - Marco Benedetti, Gennaro Catapano, Francesco De Sclavis, Marco Favorito, Aldo Glielmo, Davide Magnanimi, Antonio Muci:
Black-it: A Ready-to-Use and Easy-to-Extend Calibration Kit for Agent-based Models. 4622 - Patrick K. Erdelt, Jascha Jestel:
DBMS-Benchmarker: Benchmark and Evaluate DBMS in Python. 4628 - Minas Karamanis, David Nabergoj, Florian Beutler, John A. Peacock, Uros Seljak:
pocoMC: A Python package for accelerated Bayesian inference in astronomy and cosmology. 4634 - Adrian A. Correndo, Luiz H. Moro Rosso, Carlos Hernández, Leonardo M. Bastos, Luciana Nieto, Dean P. Holzworth, Ignacio Antonio Ciampitti:
metrica: an R package to evaluate prediction performance of regression and classification point-forecast models. 4655 - David Neudecker, Michael Joos, Muhammad Salihin Bin Zaol-kefli, Yuhao Lu, Niraly Mangal, Stephen Cairns:
ur-scape: harnessing data for stakeholder participation in city-making processes. 4664 - Dominique G. Maucieri:
quadcleanR: An R Package for the Cleanup and Visualization of Quadrat Data. 4674 - Håkon Kaspersen, Eve Zeyl Fiskebeck:
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis. 4677 - Mitchell Z. Abrams, Cameron R. Bass:
fars_cleaner: A Python package for downloading and pre-processing vehicle fatality data in the US. 4678 - Sota Yoshida:
NuclearToolkit.jl: A Julia package for nuclear structure calculations. 4694 - Connor Donegan:
geostan: An R package for Bayesian spatial analysis. 4716 - Karl-Ludwig Besser, Eduard A. Jorswieck:
QMKPy: A Python Testbed for the Quadratic Multiple Knapsack Problem. 4718 - Isabel Pietka, Ralf Drautz, Thomas Hammerschmidt:
strucscan: A lightweight Python-based framework for high-throughput material simulation. 4719 - Vladimir Nikolic, Parham Kazemi, Lauren Coombe, Johnathan Wong, Amirhossein Afshinfard, Justin Chu, René L. Warren, Inanç Birol:
btllib: A C++ library with Python interface for efficient genomic sequence processing. 4720 - Paul K. Romano, Nicolas E. Stauff, Zhiee Jhia Ooi, Yinbin Miao, Amanda Lund, Ling Zou:
WATTS: Workflow and template toolkit for simulation. 4735 - Xinyi Guan, Zeng Ren, Claire Pelofi:
py2lispIDyOM: A Python package for the information dynamics of music (IDyOM) model. 4738 - Aaron T. L. Lun:
basilisk: a Bioconductor package for managing Python environments. 4742 - Marie Roald, Yngve Mardal Moe:
TLViz: Visualising and analysing tensor decomposition models with Python. 4754 - Aman Modi, Giorgio Gonnella:
Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy. 4755 - Christopher R. Martin, Joseph A. Ranalli, Jacob P. Moore:
PYroMat: A Python package for thermodynamic properties. 4757 - Abraham Stroschein, Ian Delgadillo Bonequi, Lucas J. Koerner:
Pyripherals: A Python Package for Communicating with Peripheral Electronic Devices. 4762 - Benjamin M. Skinner:
Nuclear Morphology Analysis 2.0.0: Improved image analysis software for measuring nuclear shape. 4767 - Ali R. Vahdati, Carlos J. Melián:
EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics. 4775 - Matteo Caorsi, Raphael Reinauer, Nicolas Berkouk:
giotto-deep: A Python Package for Topological Deep Learning. 4846 - Luca Curcuraci, Richard Weinkamer, Luca Bertinetti:
bmiptools: BioMaterials Image Processing Tools. 4859 - Magnus G. Jespersen, Andrew Hayes, Mark R. Davies:
Corekaburra: pan-genome post-processing using core gene synteny. 4910
Volume 7, Number 80, December 2022
- Max Pumperla, Daniel E. Cahall:
Elephas: Distributed Deep Learning with Keras & Spark. 4073 - Zebulun W. Arendsee, Amy L. Vincent Baker, Tavis K. Anderson:
smot: a python package and CLI tool for contextual phylogenetic subsampling. 4193 - Urban Fasel, Nicola Fonzi, Andrea Iannelli, Steven L. Brunton:
FlexWing-ROM: A matlab framework for data-driven reduced-order modeling of flexible wings. 4211 - Annabelle Harvey, Guillaume Dumas:
PyNM: a Lightweight Python implementation of Normative Modeling. 4321 - Clément Agret, Annie Chateau, Gaëtan Droc, Gautier Sarah, Manuel Ruiz, Alban Mancheron:
RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes. 4363 - Elena Ranguelova, Christiaan Meijer, Leon C. Oostrum, Yang Liu, Patrick Bos, Giulia Crocioni, Matthieu Laneuville, Bryan Cardenas Guevara, Rena Bakhshi, Damian Podareanu:
DIANNA: Deep Insight And Neural Network Analysis. 4493 - Konstantin Sering, Marc Weitz, Elnaz Shafaei-Bajestan, David-Elias Künstle:
pyndl: Naïve Discriminative Learning in Python. 4515 - Rupesh Jeyaram, Suniti Sanghavi, Christian Frankenberg:
vSmartMOM.jl: an Open-Source Julia Package for Atmospheric Radiative Transfer and Remote Sensing Tools. 4575 - Jeongbin Park, Gilles Duvert, Alain Coulais, Gregory V. Jung, Sylwester Arabas, Brian Barker, Takeshi Enomoto, Sylvain Flinois, Oliver Gressel, Tomas Hillberg, Thibault Huillet, Jan Kohnert, Orion Poplawski, Eloi Rozier de Linage, Remi A. Solås, Luke Stagner, Ole Streicher, James Tappin, Thierry Thomas, Jingwei Wang, Christian Wimmer:
GNU Data Language 1.0: a free/libre and open-source drop-in replacement for IDL/PV-WAVE. 4633 - Anthony A. Gatti, Siavash Khallaghi:
PyCPD: Pure NumPy Implementation of the Coherent Point Drift Algorithm. 4681 - Robert Challen:
dtrackr: An R package for tracking the provenance of data. 4707 - Tangi Migot, Dominique Orban, Abel Soares Siqueira:
PDENLPModels.jl: An NLPModel API for Optimization Problems with PDE-Constraints. 4736 - Pierre-Yves de Müllenheim, Arnaud Chambellan:
activAnalyzer: An R Shiny app to analyse ActiGraph accelerometer data and to implement the use of the PROactive Physical Activity in COPD instruments. 4741 - Saad Yalouz, Martin Rafael Gullin, Sajanthan Sekaran:
QuantNBody: a Python package for quantum chemistry and physics to build and manipulate many-body operators and wave functions. 4759 - Bruno A. Lima, Filipe Pinto Reis:
histoc: Histocompatibility analysis performed by kidney allocation systems. 4807 - Ville Yrjänä:
DearEIS - A GUI program for analyzing impedance spectra. 4808 - Irea Mosquera-Lois, Seán R. Kavanagh, Aron Walsh, David O. Scanlon:
ShakeNBreak: Navigating the defect configurational landscape. 4817 - Aleksandra Pachalieva, Robert S. Pavel, Javier E. Santos, Abdourahmane Diaw, Nicholas Lubbers, Mohammed Mehana, Jeffrey R. Haack, Hari S. Viswanathan, Daniel Livescu, Timothy C. Germann, Christoph Junghans:
GLUE Code: A framework handling communication and interfaces between scales. 4822 - Sebastian Zieba, Laura Kreidberg:
PACMAN: A pipeline to reduce and analyze Hubble Wide Field Camera 3 IR Grism data. 4838 - Eric L. Denovellis, Maxym Myroshnychenko, Mehrad Sarmashghi, Emily P. Stephen:
Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU. 4840 - Matthew D. Parno, Paul-Baptiste Rubio, Daniel Sharp, Michael Brennan, Ricardo Baptista, Henning Bonart, Youssef M. Marzouk:
MParT: Monotone Parameterization Toolkit. 4843 - Yiqun T. Chen, Brian D. Williamson, Taylor Okonek, Charles J. Wolock, Andrew J. Spieker, Travis Y. Hee Wai, James P. Hughes, Scott S. Emerson, Amy Willis:
rigr: Regression, Inference, and General Data Analysis Tools in R. 4847 - Robert A. Caulk, Elin Törnquist, Matthias Voppichler, Andrew R. Lawless, Ryan McMullan, Wagner Costa Santos, Timothy C. Pogue, Johan van der Vlugt, Stefan P. Gehring, Pascal Schmidt:
FreqAI: generalizing adaptive modeling for chaotic time-series market forecasts. 4864 - Matthew Andres Moreno, Emily L. Dolson, Charles Ofria:
hstrat: a Python Package for phylogenetic inference on distributed digital evolution populations. 4866 - Oliver R. A. Dunbar, Ignacio Lopez-Gomez, Alfredo Garbuno-Iñigo, Daniel Zhengyu Huang, Eviatar Bach, Jin-Long Wu:
EnsembleKalmanProcesses.jl: Derivative-free ensemble-based model calibration. 4869 - Ekaterina Landgren, Alice Nadeau:
SWAMPE: A Shallow-Water Atmospheric Model in Python for Exoplanets. 4872 - Joey McCollum, Robert Turnbull:
teiphy: A Python Package for Converting TEI XML Collations to NEXUS and Other Formats. 4879 - William Pettersson:
kep_solver: A Python package for kidney exchange programme exploration. 4881 - Lucas H. McCabe:
cosasi: Graph Diffusion Source Inference in Python. 4894 - Christopher Pockrandt, Aleksey V. Zimin, Steven L. Salzberg:
Metagenomic classification with KrakenUniq on low-memory computers. 4908 - Andre Gosselink, Tatsiana Hofer, Elvira Criado-Moronati, Arndt von Haeseler, Jutta Kollet:
InspectorCell: Finding Ground Truth in Multiplexed Microscopy Images. 4949 - T. Phuong Quan:
daiquiri: Data Quality Reporting for Temporal Datasets. 5034
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