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ORCIDJournal of Open Source Software, Volume 6
Volume 6, Number 57, January 2021
- Andrea Arcuri
, Juan Pablo Galeotti, Bogdan Marculescu, Man Zhang:
EvoMaster: A Search-Based System Test Generation Tool. 2153 - Shubhadeep Sadhukhan, Shashwat Bhattacharya, Mahendra K. Verma:
fastSF: A parallel code for computing the structure functions of turbulence. 2185 - Marine Martin-Lagarde, Christophe Cossou, René Gastaud:
Exonoodle: Synthetic time-series spectra generator for transiting exoplanets. 2287 - Benjamin Michaud, Mickaël Begon:
biorbd: A C++, Python and MATLAB library to analyze and simulate the human body biomechanics. 2562 - Keith J. Roberts, Rafael dos Santos Gioria, William J. Pringle:
SeismicMesh: Triangular meshing for seismology. 2687 - Sebastian Haan:
GeoBO: Python package for Multi-Objective Bayesian Optimisation and Joint Inversion in Geosciences. 2690 - Florian Faucher:
hawen: time-harmonic wave modeling and inversion using hybridizable discontinuous Galerkin discretization. 2699 - Gustave Coste, Yannick Biard, Philippe Roux, Arnaud Hélias:
ELDAM: A Python software for Life Cycle Inventory data management. 2765 - Sebastian Kokott, Iker Hurtado, Christian Vorwerk, Claudia Draxl, Volker Blum, Matthias Scheffler:
GIMS: Graphical Interface for Materials Simulations. 2767 - Ryo Kobayashi:
nap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentials. 2768 - Luke Zoltan Kelley:
kalepy: a Python package for kernel density estimation, sampling and plotting. 2784 - Henry Senyondo, Daniel J. McGlinn, Pranita Sharma, David J. Harris, Hao Ye, Shawn D. Taylor, Jeroen Ooms, Francisco J. Rodríguez-Sanchez, Karthik Ram, Apoorva Pandey, Harshit Bansal, Max Pohlman, Ethan P. White:
Rdataretriever: R Interface to the Data Retriever. 2800 - Arianna I. Krinos, Sarah K. Hu, Natalie R. Cohen, Harriet Alexander:
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes. 2817 - Jens Eriksson, Daniel Styrström, Mikael E. Sellin:
Cellocity: A Python package for analysis of confluent cell layer dynamics. 2818 - Vincent A. Landau, Viral B. Shah, Ranjan Anantharaman, Kimberly R. Hall:
Omniscape.jl: Software to compute omnidirectional landscape connectivity. 2829 - Léo Simpson, Patrick L. Combettes, Christian L. Müller:
c-lasso - a Python package for constrained sparse and robust regression and classification. 2844 - Seb Dalgarno:
shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs). 2848 - Damien Marsic:
Parent-map: analysis of parental contributions to evolved or engineered protein or DNA sequences. 2864 - Hugo Ledoux, Filip Biljecki, Balázs Dukai, Kavisha Kumar, Ravi Y. Peters, Jantien E. Stoter, Tom Commandeur:
3dfier: automatic reconstruction of 3D city models. 2866 - Gabriel Dansereau, Timothée Poisot:
SimpleSDMLayers.jl and GBIF.jl: A Framework for Species Distribution Modeling in Julia. 2872 - M. Hakan Satman, Shreesh Adiga, Guillermo Angeris, Emre Akadal:
LinRegOutliers: A Julia package for detecting outliers in linear regression. 2892 - John Huddleston, James Hadfield, Thomas R. Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin, Elias Harkins, Trevor Bedford, Richard A. Neher, Emma B. Hodcroft:
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. 2906 - William Michael Landau:
The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing. 2959
Volume 6, Number 58, February 2021
- Florian Rhiem:
SampleDB: A sample and measurement metadata database. 2107 - Jordan Perr-Sauer, Mike Optis, Jason M. Fields, Nicola Bodini, Joseph C. y. Lee, Austin Todd, Eric Simley, Robert Hammond, Caleb Phillips, Monte Lunacek, Travis W. Kemper, Lindy Williams, Anna Craig, Nathan Agarwal, Shawn Sheng, John Meissner:
OpenOA: An Open-Source Codebase For Operational Analysis of Wind Farms. 2171 - Alex Mikes, Katherine Edmonds, Robert B. Stone, Bryony DuPont:
AutoFunc: A Python package for automating and verifying functional modeling. 2362 - Praneeth Balakrishna, Gerrit Book, Wilhelm Kirchgässner, Maximilian Schenke, Arne Traue, Oliver Wallscheid:
gym-electric-motor (GEM): A Python toolbox for the simulation of electric drive systems. 2498 - James W. Nightingale, Richard G. Hayes, Matthew Griffiths:
PyAutoFit: A Classy Probabilistic Programming Language for Model Composition and Fitting. 2550 - Eugene Huang, Adam Skoufis, Terence Denning, Jianzhong Qi, Raymond R. Dagastine, Rico F. Tabor, Joseph D. Berry:
OpenDrop: Open-source software for pendant drop tensiometry & contact angle measurements. 2604 - Michael T. Fitzgerald, Edward Gomez, Saeed Salimpour, Joe Singleton, Ridlo W. Wibowo:
"astrosource": automating optical astronomy measurement, calibration and analysis for variable stellar sources from provided photometry. 2641 - Jeffrey S. Hazboun, Brent Shapiro-Albert, Paul T. Baker, Amelia M. Henkel, Cassidy M. Wagner, Jacob Hesse, Paul R. Brook, Michael T. Lam, Maura Mclaughlin, Nathaniel Garver-Daniels:
The Pulsar Signal Simulator: A Python package for simulating radio signal data from pulsars. 2757 - Tobias Olsson, Morgan Ericsson, Anna Wingkvist:
s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques. 2791 - The Pencil Code Collaboration, Axel Brandenburg, Anders Johansen, Philippe A. Bourdin, Wolfgang Dobler, Wladimir Lyra, Matthias Rheinhardt, Sven Bingert, Nils Erland L. Haugen, Antony Mee, Frederick Gent, Natalia Babkovskaia, Chao-Chin Yang, Tobias Heinemann, Boris Dintrans, Dhrubaditya Mitra, Simon Candelaresi, Jörn Warnecke, Petri J. Käpylä, Andreas Schreiber, Piyali Chatterjee, Maarit J. Käpylä, Xiang-Yu Li, Jonas Krüger, Jørgen R. Aarnes, Graeme R. Sarson, Jeffrey S. Oishi, Jennifer Schober, Raphaël Plasson, Christer Sandin, Ewa Karchniwy, Luiz Felippe S. Rodrigues, Alexander Hubbard, Gustavo Guerrero, Andrew Snodin, Illa R. Losada, Johannes Pekkilä, Chengeng Qian:
The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained. 2807 - Claudio Zandonella Callegher, Giulia Bertoldo, Enrico Toffalini, Anna Vesely, Angela Andreella, Massimiliano Pastore, Gianmarco Altoé:
PRDA: An R package for Prospective and Retrospective Design Analysis. 2810 - Lukas Heinrich, Matthew Feickert, Giordon Stark, Kyle Cranmer:
pyhf: pure-Python implementation of HistFactory statistical models. 2823 - James W. Nightingale, Richard G. Hayes, Ashley Kelly, Aristeidis Amvrosiadis, Amy Etherington, Qiuhan He, Nan Li, XiaoYue Cao, Jonathan Frawley, Shaun Cole, Andrea Enia, Carlos S. Frenk, David R. Harvey, Ran Li, Richard J. Massey, Mattia Negrello, Andrew Robertson:
PyAutoLens: Open-Source Strong Gravitational Lensing. 2825 - Vahid S. Bokharaie:
MiTfAT: A Python-based Analysis Tool for Molecular fMRI Experiments. 2827 - Brian M. de Silva, Krithika Manohar, Emily Clark, Bingni W. Brunton, J. Nathan Kutz, Steven L. Brunton:
PySensors: A Python package for sparse sensor placement. 2828 - Robert Morgan, Brian Nord, Simon Birrer, Joshua Yao-Yu Lin, Jason Poh:
deeplenstronomy: A dataset simulation package for strong gravitational lensing. 2854 - Jannis M. Hoch, Sophie de Bruin, Niko Wanders:
CoPro: a data-driven modelling framework for conflict risk projections. 2855 - Charley Gros, Andréanne Lemay, Olivier Vincent, Lucas Rouhier, Marie-Helene Bourget, Anthime Bucquet, Joseph Paul Cohen, Julien Cohen-Adad:
ivadomed: A Medical Imaging Deep Learning Toolbox. 2868 - Markus Jonsson, Stefano Ghirlanda, Johan Lind, Vera Vinken, Magnus Enquist:
Learning Simulator: A simulation software for animal and human learning. 2891 - Benjamin Michaud, Mickaël Begon:
ezc3d: An easy C3D file I/O cross-platform solution for C++, Python and MATLAB. 2911 - Adam C. Richie-Halford, Manjari Narayan, Noah Simon, Jason D. Yeatman, Ariel Rokem:
Groupyr: Sparse Group Lasso in Python. 3024
Volume 6, Number 59, March 2021
- Lydia R. Lucchesi, Petra M. Kuhnert, Christopher K. Wikle:
Vizumap: an R package for visualising uncertainty in spatial data. 2409 - Marina Manso Jimeno, John Thomas Vaughan, Sairam Geethanath:
Off-resonance CorrecTion OPen soUrce Software (OCTOPUS). 2578 - John T. Gregg, Trang T. Le, Jason H. Moore:
REGENS: an open source Python package for simulating realistic autosomal genotypes. 2743 - Kenneth Higa, Vincent S. Battaglia, Venkat Srinivasan:
PyGDH: Python Grid Discretization Helper. 2744 - Pedro Rafael Diniz Marinho:
ropenblas: Download, Compile and Link OpenBLAS Library with R. 2769 - Riley X. Brady, Aaron Spring:
climpred: Verification of weather and climate forecasts. 2781 - Robert Falck, Justin S. Gray, Kaushik Ponnapalli, Ted Wright:
dymos: A Python package for optimal control of multidisciplinary systems. 2809 - Jérôme Buisine, Samuel Delepoulle, Christophe Renaud:
Minimalist And Customisable Optimisation Package. 2812 - Adam Symington:
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories. 2824 - Florian Gacon, Christophe Godin, Olivier Ali:
BVPy: A FEniCS-based Python package to ease the expression and study of boundary value problems in Biology. 2831 - Timo Betcke, Matthew W. Scroggs:
Bempp-cl: A fast Python based just-in-time compiling boundary element library. 2879 - Kanishka Narayan, Chris R. Vernon, Stephanie Waldhoff, James A. Edmonds, Ryna Cui:
ambrosia: An R package for calculating and analyzing food demand that is responsive to changing incomes and prices. 2890 - Balaje Kalyanaraman, Michael H. Meylan, Bishnu P. Lamichhane, Luke G. Bennetts:
iceFEM: A FreeFem package for wave induced ice-shelf vibrations. 2939 - Samay Garg, Julie C. Fornaciari, Adam Z. Weber, Nemanja Danilovic:
fuelcell: A Python package and graphical user interface for electrochemical data analysis. 2940 - Krzysztof Dyba, Jakub Nowosad:
rgugik: Search and Retrieve Spatial Data from the Polish Head Office of Geodesy and Cartography in R. 2948 - Jon Schwenk, Jayaram Hariharan:
RivGraph: Automatic extraction and analysis of river and delta channel network topology. 2952 - Zeyuan Song, Anastasia Gurinovich, Anthony Federico, Stefano Monti, Paola Sebastiani:
nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline. 2957 - Qiusheng Wu:
lidar: A Python package for delineating nested surface depressions from digital elevation data. 2965 - Wouter G. j. van Zeist, Héloïse F. Stevance, J. J. Eldridge:
Riroriro: Simulating gravitational waves and evaluating their detectability in Python. 2968 - Ghislain Vieilledent:
forestatrisk: a Python package for modelling and forecasting deforestation in the tropics. 2975 - Andrew J. Quinn, Vitor Lopes-dos-Santos, David Dupret, Anna Christina Nobre, Mark W. Woolrich:
EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python. 2977 - Jacques Serizay, Julie Ahringer:
Generating fragment density plots in R/Bioconductor with VplotR. 3009 - Andrea Bommert, Michel Lang:
stabm: Stability Measures for Feature Selection. 3010 - Wilmer Uruchi, Miguel Castrillo, Daniel Beltrán:
Autosubmit GUI: A Javascript-based Graphical User Interface to Monitor Experiments Workflow Execution. 3049 - Alessandro Cheli:
Metatheory.jl: Fast and Elegant Algebraic Computation in Julia with Extensible Equality Saturation. 3078 - Alex M. Ganose, Amy Searle, Anubhav Jain, Sinéad M. Griffin:
IFermi: A python library for Fermi surface generation and analysis. 3089
Volume 6, Number 60, April 2021
- Paul Westermann, Theodor Victor Christiaanse, Will Beckett, Paul Kovacs, Ralph Evins:
besos: Building and Energy Simulation, Optimization and Surrogate Modelling. 2677 - Derrick J. A. Chambers, M. Shawn Boltz, Calum J. Chamberlain:
ObsPlus: A Pandas-centric ObsPy expansion pack. 2696 - Robert J. Moss:
POMDPStressTesting.jl: Adaptive Stress Testing for Black-Box Systems. 2749 - Gianmarco Mengaldo, Romit Maulik:
PySPOD: A Python package for Spectral Proper Orthogonal Decomposition (SPOD). 2862 - Jost Migenda, Susan Cartwright, Liz Kneale, Matthew Malek, Yan-Jie Schnellbach, Owen Stone:
sntools: An event generator for supernova burst neutrinos. 2877 - Narayanarao Bhogapurapu, Subhadip Dey, Dipankar Mandal, Avik Bhattacharya, Y. S. Rao:
PolSAR tools: A QGIS plugin for generating SAR descriptors. 2970 - Jackson Borchardt, Raymond Dunn, Saul Kato:
minimo: a linked data and metadata storage system for small labs. 2979 - Alejandra M. Martínez, Matías Salibián Barrera:
RBF: An R package to compute a robust backfitting estimator for additive models. 2992 - Marcelo Ponce, Amit Sandhel:
covid19.analytics: An R Package to Obtain, Analyze and Visualize Data from the 2019 Coronavirus Disease Pandemic. 2995 - David Keitel, Rodrigo Tenorio, Gregory Ashton, Reinhard Prix:
PyFstat: a Python package for continuous gravitational-wave data analysis. 3000 - Johannes Buchner:
UltraNest - a robust, general purpose Bayesian inference engine. 3001 - Oluwasegun Ayokunle Somefun, Kayode Akingbade, Folasade Mojisola Dahunsi:
NLSIG-COVID19Lab: A modern logistic-growth tool (nlogistic-sigmoid) for descriptively modelling the dynamics of the COVID-19 pandemic process. 3002 - Michael L. Waskom:
seaborn: statistical data visualization. 3021 - Giulio Fabbian, Julien Peloton:
Simulating instrumental systematics of Cosmic Microwave Background experiments with s4cmb. 3022 - Robert A. Shaw, J. Grant Hill:
libecpint: A C++ library for the efficient evaluation of integrals over effective core potentials. 3039 - Yaron Gvili:
LibSWIFFT - A fast C/C++ Library for the SWIFFT Secure Homomorphic Hash Function. 3040 - Eike Caldeweyher:
kallisto: A command-line interface to simplify computational modelling and the generation of atomic features. 3050 - Vikram Baliga:
gaussplotR: Fit, Predict and Plot 2D-Gaussians in R. 3074 - Farshid Tavakolizadeh, Shreekantha Devasya:
Thing Directory: Simple and lightweight registry of IoT device metadata. 3075 - Nils Kroell:
imea: A Python package for extracting 2D and 3D shape measurements from images. 3091 - Clemens Schmid, Stephan Schiffels:
bleiglas: An R package for interpolation and visualisation of spatiotemporal data with 3D tessellation. 3092 - Benjamin F. Maier:
epipack: An infectious disease modeling package for Python. 3097 - Gabriele Bozzola:
kuibit: Analyzing Einstein Toolkit simulations with Python. 3099 - Alan Haynes, Armando Lenz, Odile Stalder, Andreas Limacher:
presize: An R-package for precision-based sample size calculation in clinical research. 3118 - Taylor Griswold, Curtis Kapsak, Jessica C. Chen, Henk C. den Bakker, Grant Williams, Alyssa Kelley, Eshaw Vidyaprakash, Lee S. Katz:
SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data. 2334 - Gael Forget:
IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system. 2813 - Antonello Lobianco:
BetaML: The Beta Machine Learning Toolkit, a self-contained repository of Machine Learning algorithms in Julia. 2849 - Saleh Rezaeiravesh, Ricardo Vinuesa, Philipp Schlatter:
UQit: A Python package for uncertainty quantification (UQ) in computational fluid dynamics (CFD). 2871 - Kevin Kramer, Johan Chang:
Visualization of Multi-Dimensional Data - The data-slicer Package. 2969 - Sam Parsons:
splithalf: robust estimates of split half reliability. 3041 - Navid C. Constantinou, Gregory LeClaire Wagner, Lia Siegelman, Brodie C. Pearson, André Palóczy:
GeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUs. 3053 - Daniel Lüdecke, Mattan S. Ben-Shachar, Indrajeet Patil, Philip D. Waggoner, Dominique Makowski:
performance: An R Package for Assessment, Comparison and Testing of Statistical Models. 3139 - Diego A. Palma, Christian Soto, Mónica Veliz, Bruno Karelovic, Bernardo Riffo:
TRUNAJOD: A text complexity library to enhance natural language processing. 3153 - William Michael Landau:
The stantargets R package: a workflow framework for efficient reproducible Stan-powered Bayesian data analysis pipelines. 3193
Volume 6, Number 61, May 2021
- Shannon Axelrod, Matthew Cai, Ambrose J. Carr, Jeremy Freeman, Deep Ganguli, Justin T. Kiggins, Brian Long, Tony Tung, Kevin A. Yamauchi:
starfish: scalable pipelines for image-based transcriptomics. 2440 - Francis Banville, Steve Vissault, Timothée Poisot:
Mangal.jl and EcologicalNetworks.jl: Two complementary packages for analyzing ecological networks in Julia. 2721 - Amir Shahmoradi, Fatemeh Bagheri:
ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran. 2741 - Steve Macenski, Ivona Jambrecic:
SLAM Toolbox: SLAM for the dynamic world. 2783 - Nelly Barret, Fabien Duchateau, Franck Favetta:
Predihood: an open-source tool for predicting neighbourhoods' information. 2805 - Vasilis N. Nikolaidis:
The nnlib2 library and nnlib2Rcpp R package for implementing neural networks. 2876 - Sebastian Kopf, Brett Davidheiser-Kroll, Ilja Kocken:
Isoreader: An R package to read stable isotope data files for reproducible research. 2878 - Andrew C. Teucher, Sam J. Albers, Stephanie L. Hazlitt:
bcdata: An R package for searching & retrieving data from the B.C. Data Catalogue. 2927 - Luka Pecnik, Iztok Fister Jr.:
NiaAML: AutoML framework based on stochastic population-based nature-inspired algorithms. 2949 - Julia Wrobel, Alexander Bauer:
registr 2.0: Incomplete Curve Registration for Exponential Family Functional Data. 2964 - Banjo Obayomi, Christopher H. Todd, Lucas Cadalzo, David Killian, Anthony C. Wong:
Magicwand: A platform to provide high-quality, reliable, and reproducible data sets for low-and-slow DDoS attacks. 3032 - Malte Brunn, Naveen Himthani, George Biros, Miriam Mehl, Andreas Mang:
CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures. 3038 - Felix Matuschke, Katrin Amunts, Markus Axer:
fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI. 3042 - Johannes Buchner:
Bayesian X-ray Analysis (BXA) v4.0. 3045 - Robert Andrew Martin:
PyPortfolioOpt: portfolio optimization in Python. 3066 - Begüm D. Topçuoglu, Zena Lapp, Kelly L. Sovacool, Evan S. Snitkin, Jenna Wiens, Patrick D. Schloss:
mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. 3073 - Yves Mocquard, Pierre Navaro, Nicolas Crouseilles:
HOODESolver.jl: A Julia package for highly oscillatory problems. 3077 - Vincent Russo:
toqito - Theory of quantum information toolkit: A Python package for studying quantum information. 3082 - Adrian Richter, Carsten Oliver Schmidt, Markus Krüger, Stephan Struckmann:
dataquieR: assessment of data quality in epidemiological research. 3093 - Dogu Kaan Eraslan:
PyGModels: A Python package for exploring Probabilistic Graphical Models with Graph Theoretical Structures. 3115 - Didier A. Murillo, Salvador A. Gezan, Ana M. Heilman, Thomas C. Walk, Johan S. Aparicio, Richard D. Horsley:
'FielDHub': A Shiny App for Design of Experiments in Life Sciences. 3122 - Sally Sun, Owen G. Ward, Jing Wu, Lihao Xiao, Xiaoxi Zhao, Tian Zheng:
ppdiag: Diagnostic Tools for Temporal Point Processes. 3133 - Tingyu Wang, Rio Yokota, Lorena A. Barba:
ExaFMM: a high-performance fast multipole method library with C++ and Python interfaces. 3145 - Yida Chen, Eric Faden, Nathan C. Ryan:
KALMUS: tools for color analysis of films. 3156 - Toshihiro Umehara:
datasailr - An R Package for Row by Row Data Processing, Using DataSailr Script. 3166 - Indrajeet Patil:
Visualizations with statistical details: The 'ggstatsplot' approach. 3167 - Katarina Brlec, Daniel W. Davies, David O. Scanlon:
Surfaxe: Systematic surface calculations. 3171 - Thomas Huet, Jose M. Pozo, Craig Alexander:
Analysis of Prehistoric Iconography with the R package iconr. 3191 - Chandan Singh, Keyan Nasseri, Yan Shuo Tan, Tiffany M. Tang, Bin Yu:
imodels: a python package for fitting interpretable models. 3192 - Chun Fai Tung, Theo Glauch, Michael James Larson, Alex Pizzuto, René Reimann, Ignacio J. Taboada:
FIRESONG: A python package to simulate populations of extragalactic neutrino sources. 3194 - Jakob Vanhoefer, Marta R. A. Matos, Dilan Pathirana, Yannik Schälte, Jan Hasenauer:
yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. 3215 - Indrajeet Patil:
statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details. 3236 - Nhat C. Tran, Jean X. Gao:
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. 3249 - Conor D. MacBride, David B. Jess:
MCALF: Multi-Component Atmospheric Line Fitting. 3265
Volume 6, Number 62, June 2021
- Jason Nance, Peter Baumgartner:
gobbli: A uniform interface to deep learning for text in Python. 2395 - Devarshi Ghoshal, Ludovico Bianchi, Abdelilah Essiari, Michael W. Beach, Drew Paine, Lavanya Ramakrishnan:
Science Capsule - Capturing the Data Life Cycle. 2484 - Egon L. Willighagen:
Bacting: a next generation, command line version of Bioclipse. 2558 - Lukas Hörtnagl:
DYCO: A Python package to dynamically detect and compensate for time lags in ecosystem time series. 2575 - Zebedee Nicholls, Jared Lewis:
OpenSCM Two Layer Model: A Python implementation of the two-layer climate model. 2766 - James D. Gaboardi, Sergio J. Rey, Stefanie Lumnitz:
spaghetti: spatial network analysis in PySAL. 2826 - Michael Hirsch:
h5fortran: object-oriented polymorphic Fortran interface for HDF5 file IO. 2842 - Ekaterina Ilin:
AltaiPony - Flare science in Kepler, K2 and TESS light curves. 2845 - Marcus Dansarie:
sboxgates: A program for finding low gate count implementations of S-boxes. 2946 - Sophie Theis, Magali Suzanne, Guillaume Gay:
Tyssue: an epithelium simulation library. 2973 - Hadrien Titeux, Rachid Riad:
pygamma-agreement: Gamma $\gamma$ measure for inter/intra-annotator agreement in Python. 2989 - Stefan McCabe, Leo Torres, Timothy LaRock, Syed Arefinul Haque, Chia-Hung Yang, Harrison Hartle, Brennan Klein:
netrd: A library for network reconstruction and graph distances. 2990 - Alexander Fabisch:
gmr: Gaussian Mixture Regression. 3054 - Tianbai Xiao:
Kinetic.jl: A portable finite volume toolbox for scientific and neural computing. 3060 - Joël Foramitti:
AgentPy: A package for agent-based modeling in Python. 3065 - Apostolos Spanakis-Misirlis, Cameron L. Van Eck, E. P. Boven:
Virgo: A Versatile Spectrometer for Radio Astronomy. 3067 - Jeffrey S. Oishi, Keaton J. Burns, Susan E. Clark, Evan H. Anders, Benjamin P. Brown, Geoffrey M. Vasil, Daniel Lecoanet:
eigentools: A Python package for studying differential eigenvalue problems with an emphasis on robustness. 3079 - Hansen Johnson, Daniel Morrison, Christopher Taggart:
WhaleMap: a tool to collate and display whale survey results in near real-time. 3094 - Shih-Yun Tang, Asa G. Stahl, Christopher M. Johns-Krull, Lisa Prato, Joe Llama:
IGRINS RV: A Python Package for Precision Radial Velocities with Near-Infrared Spectra. 3095 - Pi-Yueh Chuang, Tracy Thorleifson, Lorena A. Barba:
geoclaw-landspill: an oil land-spill and overland flow simulator for pipeline rupture events. 3114 - Anders Markvardsen, Tyrone Rees, Michael Wathen, Andrew Lister, Patrick Odagiu, Atijit Anuchitanukul, Tom Farmer, Anthony Lim, Federico Montesino, Tim Snow, Andrew McCluskey:
'FitBenchmarking': an open source 'Python' package comparing data fitting software. 3127 - David Montero:
eemont: A Python package that extends Google Earth Engine. 3168 - Jens Lange:
CliquePercolation: An R Package for conducting and visualizing results of the clique percolation network community detection algorithm. 3210 - Travis Thurber, Chris R. Vernon, Ning Sun, Sean W. D. Turner, Jim Yoon, Nathalie Voisin:
mosartwmpy: A Python implementation of the MOSART-WM coupled hydrologic routing and water management model. 3221 - Tobias Schoch:
wbacon: Weighted BACON algorithms for multivariate outlier nomination (detection) and robust linear regression. 3238 - Mathew Jacob:
Eir: A Python Package for Epidemic Simulation. 3247 - Christopher Barrie, Justin Chun-Ting Ho:
academictwitteR: an R package to access the Twitter Academic Research Product Track v2 API endpoint. 3272 - Diego R. Barneche, Greg Coleman, Duncan Fermor, Eduardo Klein, Tobias Robinson, Jason Smith, Jeffrey L. Sheehan, Shannon Dowley, Dean Ditton, Kevin Gunn, Gavin Ericson, Murray Logan, Mark Rehbein:
dataaimsr: An R Client for the Australian Institute of Marine Science Data Platform API which provides easy access to AIMS Data Platform. 3282 - Simon Birrer, Anowar J. Shajib, Daniel Gilman, Aymeric Galan, Jelle Aalbers, Martin Millon, Robert Morgan, Giulia Pagano, Ji Won Park, Luca Teodori, Nicolas Tessore, Madison Ueland, Lyne Van de Vyvere, Sebastian Wagner-Carena, Ewoud Wempe, Lilan Yang, Xuheng Ding, Thomas Schmidt, Dominique Sluse, Ming Zhang, Adam Amara:
lenstronomy II: A gravitational lensing software ecosystem. 3283 - Marc Schönwiesner, Ole Bialas:
s(ound)lab: An easy to learn Python package for designing and running psychoacoustic experiments. 3284 - Daniel Foreman-Mackey, Rodrigo Luger, Eric Agol, Thomas Barclay, Luke G. Bouma, Timothy D. Brandt, Ian Czekala, Trevor J. David, Jiayin Dong, Emily A. Gilbert, Tyler A. Gordon, Christina Hedges, Daniel Hey, Brett M. Morris, Adrian M. Price-Whelan, Arjun B. Savel:
'exoplanet': Gradient-based probabilistic inference for exoplanet data & other astronomical time series. 3285 - Fabian Hofmann, Johannes Hampp, Fabian Neumann, Tom Brown, Jonas Hörsch:
atlite: A Lightweight Python Package for Calculating Renewable Power Potentials and Time Series. 3294 - Batuhan Taskaya:
Reiz: Structural Source Code Search. 3296 - Christoph Wick, Benjamin Kühn, Gundram Leifert, Konrad Sperfeld, Tobias Strauß, Jochen Zöllner, Tobias Grüning:
_tfaip_ - a Generic and Powerful Research Framework for Deep Learning based on Tensorflow. 3297
Volume 6, Number 63, July 2021
- Jed Brown, Ahmad Abdelfattah, Valeria Barra, Natalie N. Beams, Jean-Sylvain Camier, Veselin Dobrev, Yohann Dudouit, Leila Ghaffari, Tzanio V. Kolev, David S. Medina, Will Pazner, Thilina Rathnayake, Jeremy L. Thompson, Stan Tomov:
libCEED: Fast algebra for high-order element-based discretizations. 2945 - Jean M. Sexton, Zarija Lukic, Ann S. Almgren, Christopher S. Daley, Brian Friesen, Andrew Myers, Weiqun Zhang:
Nyx: A Massively Parallel AMR Code for Computational Cosmology. 3068 - Rodrigo Luger, Daniel Foreman-Mackey, Christina Hedges:
starry_process: Interpretable Gaussian processes for stellar light curves. 3071 - Robin Trama, Christophe A. Hautier, Yoann Blache:
fctSnPM: Factorial ANOVA and post-hoc tests for Statistical nonParametric Mapping in MATLAB. 3159 - David J. M. Barnett, Ilja C. W. Arts, John Penders:
microViz: an R package for microbiome data visualization and statistics. 3201 - David Shaw, Nicola Carslaw:
INCHEM-Py: An open source Python box model for indoor air chemistry. 3224 - Yaroslav O. Halchenko, Kyle Meyer, Benjamin Poldrack, Debanjum Singh Solanky, Adina S. Wagner, Jason Gors, Dave MacFarlane, Dorian Pustina, Vanessa V. Sochat, Satrajit S. Ghosh, Christian Mönch, Christopher J. Markiewicz, Laura Waite, Ilya Shlyakhter, Alejandro de la Vega, Soichi Hayashi, Christian Olaf Häusler, Jean-Baptiste Poline, Tobias Kadelka, Kusti Skytén, Dorota Jarecka, David N. Kennedy, Ted J. Strauss, Matt Cieslak, Peter Vavra, Horea-Ioan Ioanas, Robin Schneider, Mika Pflüger, James V. Haxby, Simon B. Eickhoff, Michael Hanke:
DataLad: distributed system for joint management of code, data, and their relationship. 3262 - Joseph Palmer, Katharine Sherratt, Richard Martin-Nielson, Jonnie Bevan, Hamish Gibbs, LSHTM CMMID COVID-19 Working Group, Sebastian Funk, Sam Abbott:
covidregionaldata: Subnational data for COVID-19 epidemiology. 3290 - Andrew P. Smith:
neworder: a dynamic microsimulation framework for Python. 3351 - Swetanshu Tandon, Wolfgang Schmitt, Graeme Watson:
J2suscep: Calculation of magnetic exchange coupling and temperature dependence of magnetic susceptibility. 2838 - Tom Grylls, Ivo Suter, Birgit Sützl, Sam Owens, David Meyer, Maarten van Reeuwijk:
uDALES: large-eddy-simulation software for urban flow, dispersion, and microclimate modelling. 3055 - Vyas Ramasubramani, Bradley D. Dice, Tobias Dwyer, Sharon C. Glotzer:
coxeter: A Python package for working with shapes. 3098 - Justin Shenk, Wolf Byttner, Saranraj Nambusubramaniyan, Alexander Zoeller:
Traja: A Python toolbox for animal trajectory analysis. 3202 - James Burgess, Francesca Capel:
popsynth: A generic astrophysical population synthesis framework. 3257 - Philippe Boileau, Nima S. Hejazi, Brian Collica, Mark J. van der Laan, Sandrine Dudoit:
cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R. 3273 - Thomas P. Urbach, Andrey Portnoy:
fitgrid: A Python package for multi-channel event-related time series regression modeling. 3293 - Vanessa V. Sochat, Alec Scott:
Collaborative Container Modules with Singularity Registry HPC. 3311 - Nguyen Huynh, Sergio Béjar, Vineeta Yadav, Bumba Mukherjee:
IDCeMPy: Python Package for Inflated Discrete Choice Models. 3322 - Anna Jenul, Stefan Schrunner, Bao Huynh, Oliver Tomic:
RENT: A Python Package for Repeated Elastic Net Feature Selection. 3323 - Meinard Müller, Frank Zalkow:
libfmp: A Python Package for Fundamentals of Music Processing. 3326 - Philipp Lucas, Joachim Giesen:
Lumen: A software for the interactive visualization of probabilistic models together with data. 3395 - Qiusheng Wu:
Leafmap: A Python package for interactive mapping and geospatial analysis with minimal coding in a Jupyter environment. 3414 - Adithi R. Upadhya, Pratyush Agrawal, Sreekanth Vakacherla, Meenakshi Kushwaha:
pollucheck v1.0: A package to explore open-source air pollution data. 3435 - Pratheesh P. Gopinath, Rajender Parsad, Brigit Joseph, Adarsh S.:
grapesAgri1: Collection of Shiny Apps for Data Analysis in Agriculture. 3437 - Mikkel Meyer Andersen, Søren Højsgaard:
caracas: Computer algebra in R. 3438
Volume 6, Number 64, August 2021
- Roshan Samuel, Shashwat Bhattacharya, Ali Asad, Soumyadeep Chatterjee, Mahendra K. Verma, Ravi Samtaney, Syed Anwer:
SARAS: A general-purpose PDE solver for fluid dynamics. 2095 - Kevin Shook, Raymond J. Spiteri, John W. Pomeroy, Tonghe Liu, Oluwaseun Sharomi:
WDPM: the Wetland DEM Ponding Model. 2276 - Nikolaos D. Kallimanis:
Synch: A framework for concurrent data-structures and benchmarks. 3143 - Peer Herholz, Rita Ludwig, Jean-Baptiste Poline:
BIDSonym: a BIDS App for the pseudo-anonymization of neuroimaging datasets. 3169 - Luca Congedo:
Semi-Automatic Classification Plugin: A Python tool for the download and processing of remote sensing images in QGIS. 3172 - E. Arellano, Niklas Wulff, B. Fuchs, W. Hu:
autumn: A Python library for dynamic modelling of captured CO~2~ cost potential curves. 3203 - Christoph Lehrenfeld, Fabian Heimann, Janosch Preuß, Henry von Wahl:
ngsxfem: Add-on to NGSolve for geometrically unfitted finite element discretizations. 3237 - Liangliang Nan:
Easy3D: a lightweight, easy-to-use, and efficient C++ library for processing and rendering 3D data. 3255 - Jon. T. Drobny, Davide Curreli:
RustBCA: A High-Performance Binary-Collision-Approximation Code for Ion-Material Interactions. 3298 - Amanda Smith, Benjamin Stürmer, Travis Thurber, Chris R. Vernon:
diyepw: A Python package for Do-It-Yourself EnergyPlus weather file generation. 3313 - Ulf A. Hamster:
bwsample: Processing Best-Worst Scaling data. 3324 - Andrew Hails, Adam Day:
The SAGE Rejected Article Tracker. 3348 - Cameron T. Roots, Alexandra Lukasiewicz, Jeffrey E. Barrick:
OSTIR: open source translation initiation rate prediction. 3362 - Gaurav Vaidya, Nico Cellinese, Hilmar Lapp:
JPhyloRef: a tool for testing and resolving phyloreferences. 3374 - Mamadou Diallo:
samplics: a Python Package for selecting, weighting and analyzing data from complex sampling designs. 3376 - Eleftherios Garyfallidis, Serge Koudoro, Javier Guaje, Marc-Alexandre Côté, Soham Biswas, David Reagan, Nasim Anousheh, Filipi N. Silva, Geoffrey C. Fox, FURY Contributors:
FURY: advanced scientific visualization. 3384 - Jacob Merson, Mark S. Shephard:
model-traits: Model attribute definitions for scientific simulations in C++. 3389 - Daniel Lüdecke, Indrajeet Patil, Mattan S. Ben-Shachar, Brenton M. Wiernik, Philip D. Waggoner, Dominique Makowski:
see: An R Package for Visualizing Statistical Models. 3393 - Xavier Casas Moreno, Staffan Al-Kadhimi, Jonatan Alvelid, Andreas Bodén, Ilaria Testa:
ImSwitch: Generalizing microscope control in Python. 3394 - Karin Knudson, Gabe Schoenbach, Amariah Becker:
PyEI: A Python package for ecological inference. 3397 - Andrew Moodie, Jayaram Hariharan, Eric Barefoot, Paola Passalacqua:
pyDeltaRCM: a flexible numerical delta model. 3398 - Edward Rusu, Ruben Glatt:
Abmarl: Connecting Agent-Based Simulations with Multi-Agent Reinforcement Learning. 3424 - Meinard Müller, Yigitcan Özer, Michael Krause, Thomas Prätzlich, Jonathan Driedger:
Sync Toolbox: A Python Package for Efficient, Robust, and Accurate Music Synchronization. 3434 - Pablo Gómez, Håvard Toftevaag, Gabriele Meoni:
torchquad: Numerical Integration in Arbitrary Dimensions with PyTorch. 3439 - Philippe Rast, Stephen Martin:
bmgarch: An R-Package for Bayesian Multivariate GARCH models. 3452 - Florian Pfisterer, Christoph Kern, Susanne Dandl, Matthew Sun, Michael Kim, Bernd Bischl:
mcboost: Multi-Calibration Boosting for R. 3453 - Hendrik Ranocha:
SummationByPartsOperators.jl: A Julia library of provably stable discretization techniques with mimetic properties. 3454 - Walker Arce, James Gehringer:
Biosensor Framework: A C# Library for Affective Computing. 3455 - George G. Vega Yon:
Building, Importing, and Exporting GEXF Graph Files with rgexf. 3456 - Sacha Schutz, Charles Monod-Broca, Anne-Sophie Denommé-Pichon:
CutePeaks: A modern viewer for Sanger trace file. 3457 - Derryn Knife:
SurPyval: Survival Analysis with Python. 3484 - James Hester, Erez Shinan:
Lerche: Generating data file processors in Julia from EBNF grammars. 3497 - Nils Lüttschwager:
NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals. 3526 - Tom Westerhout:
lattice-symmetries: A package for working with quantum many-body bases. 3537 - Matthew W. Scroggs:
Symfem: a symbolic finite element definition library. 3556 - Radek Lonka, Francesca Verones, Konstantin Stadler:
The MarINvaders Toolkit. 3575 - Monsuru Adepeju:
R-Opitools - An Opinion Analytical Tool for Big Digital Text Document (DTD). 3605
Volume 6, Number 65, September 2021
- Kristen Yeh, Sophie Castel, Naomi Stock, Theresa Stotesbury, Wesley Burr:
subMALDI: an open framework R package for processing irregularly-spaced mass spectrometry data. 2694 - David Meyer, Thomas Nagler:
Synthia: multidimensional synthetic data generation in Python. 2863 - Isaías Rodríguez, Renela Valladares, Alexander Valladares, David Hinojosa-Romero, Ulises Santiago, Ariel Valladares:
Correlation: An Analysis Tool for Liquids and for Amorphous Solids. 2976 - Benjamin Miquel:
Coral: a parallel spectral solver for fluid dynamics and partial differential equations. 2978 - Prashant K. Jha, Patrick Diehl:
NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models. 3020 - Mengqi Zhao, Matthew Binsted, Thomas Wild, Zarrar Khan, Brinda Yarlagadda, Gokul Iyer, Chris R. Vernon, Pralit Patel, Sílvia da Silva, Katherine V. Calvin:
plutus: An R package to calculate electricity investments and stranded assets from the Global Change Analysis Model (GCAM). 3212 - Simon Danisch, Julius Krumbiegel:
Makie.jl: Flexible high-performance data visualization for Julia. 3349 - Barak Shoshany:
OGRe: An Object-Oriented General Relativity Package for Mathematica. 3416 - Dion Häfner, Filippo Vicentini:
mpi4jax: Zero-copy MPI communication of JAX arrays. 3419 - Mehmet Satman, Bahadir Yildirim, Ersagun Kuruca:
JMcDM: A Julia package for multiple-criteria decision-making tools. 3430 - Riccardo Biondi, Nico Curti, Enrico Giampieri, Gastone C. Castellani:
COVID-19 Lung Segmentation. 3447 - Matthew L. Evans, Casper Andersen, Shyam Dwaraknath, Markus Scheidgen, Ádám Fekete, Donald Winston:
optimade-python-tools: a Python library for serving and consuming materials data via OPTIMADE APIs. 3458 - Mathias Goncalves, Christopher J. Markiewicz, Stefano Moia, Satrajit S. Ghosh, Russell A. Poldrack, Oscar Esteban:
NiTransforms: A Python tool to read, represent, manipulate, and apply dimensional spatial transforms. 3459 - Phoebe Pearce:
RayFlare: flexible optical modelling of solar cells. 3460 - Satej Soman, Caitlin Loftus, Steven Buschbach, Manasi Phadnis, Luís M. A. Bettencourt:
epimargin: A Toolkit for Epidemiological Estimation, Prediction, and Policy Evaluation. 3464 - Thomas Goelles, Birgit Schlager, Stefan Muckenhuber, Sarah Haas, Tobias Hammer:
pointcloudset: Efficient Analysis of Large Datasets of Point Clouds Recorded Over Time. 3471 - Broncio Aguilar-Sanjuan, Víctor J. García-Garrido, Vladimír Krajnák, Shibabrat Naik, Stephen Wiggins:
LDDS: Python package for computing and visualizing Lagrangian Descriptors for Dynamical Systems. 3482 - Marcus Beck, Meagan Schrandt, Michael Wessel, Edward Sherwood, Gary Raulerson, Adhokshaja Prasad, Benjamin Best:
tbeptools: An R package for synthesizing estuarine data for environmental research. 3485 - Michael Clair, Matthew Siegler:
lhorizon: geometry and targeting via JPL Horizons. 3495 - Francesco Andreuzzi:
BisPy: Bisimulation in Python. 3519 - Hubert Santuz, Amélie Bacle, Pierre Poulain, Patrick Fuchs:
buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters. 3521 - Matt Landreman, Bharat Medasani, Florian Wechsung, Andrew Giuliani, Rogerio Jorge, Caoxiang Zhu:
SIMSOPT: A flexible framework for stellarator optimization. 3525 - Erwan Bocher, Jérémy Bernard, Elisabeth Wiederhold, François Leconte, Gwendall Petit, Sylvain Palominos, Camille Noûs:
GeoClimate: a Geospatial processing toolbox for environmental and climate studies. 3541 - Jesse Cambon, Diego Hernangómez, Christopher Belanger, Daniel Possenriede:
tidygeocoder: An R package for geocoding. 3544 - Saranraj Nambusubramaniyan:
sorn: A Python package for Self Organizing Recurrent Neural Network. 3545 - Derek Fujimoto:
bfit: A Python Application For Beta-Detected NMR. 3598 - Chris R. Vernon, Jennie S. Rice, Nino Zuljevic, Kendall L. Mongird, Kristian Nelson, Gokul Iyer, Nathalie Voisin, Matthew Binsted:
cerf: A Python package to evaluate the feasibility and costs of power plant siting for alternative futures. 3601 - Olger Siebinga:
TraViA: a Traffic data Visualization and Annotation tool in Python. 3607 - Xiao Song, Kwek Chong:
home2park: An R package to assess the spatial provision of urban parks. 3609 - Robert Luke:
AuditoryStimuli.jl: A Julia package for generating real-time auditory stimuli. 3613 - Mingze Huang, Christian L. Müller, Irina Gaynanova:
latentcor: An R Package for estimating latent correlations from mixed data types. 3634 - Grant Stevens, Sotiria Fotopoulou, Malcolm N. Bremer, Oliver Ray:
AstronomicAL: an interactive dashboard for visualisation, integration and classification of data with Active Learning. 3635 - Soledad Galli:
Feature-engine: A Python package for feature engineering for machine learning. 3642 - Antoine Diez:
SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency. 3653 - Simon Couch, Andrew Bray, Chester Ismay, Evgeni Chasnovski, Benjamin S. Baumer, Mine Çetinkaya-Rundel:
infer: An R package for tidyverse-friendly statistical inference. 3661
Volume 6, Number 66, October 2021
- Avik Pal, Aniket Das:
TorchGAN: A Flexible Framework for GAN Training and Evaluation. 2606 - Jason Rumengan, Terry Yue Zhuo, Conrad Sanderson:
PyArmadillo: a streamlined linear algebra library for Python. 3051 - Tiago Tresoldi:
Ngesh: a Python library for synthetic phylogenetic data. 3173 - Taher Chegini, Hong-Yi Li, L. Leung:
HyRiver: Hydroclimate Data Retriever. 3175 - Sunil Anandatheertha:
PXO (Poly-XTAL Operations): MATLAB Codebase to Generate, Analyse and Export Complex 2D Spatio-Temporally Gradient Grain Structures. 3190 - Francisco Costa, Andrew Clifton, Nikola Vasiljevic, Ines Würth:
Qlunc: Quantification of lidar uncertainty. 3211 - Cyrille Lavigne, Alán Aspuru-Guzik:
funsies: A minimalist, distributed and dynamic workflow engine. 3274 - Ben S. Prather, George N. Wong, Vedant Dhruv, Benjamin Ryan, Joshua C. Dolence, Sean Ressler, Charles F. Gammie:
iharm3D: Vectorized General Relativistic Magnetohydrodynamics. 3336 - Kristian Nelson, Sean W. D. Turner, Chris R. Vernon, Jennie S. Rice:
gamut: A Geospatial R Package to Analyze Multisectoral Urban Teleconnections. 3383 - Ben Young, Michael Srocka, Wesley Ingwersen, Ben Morelli, Sarah Cashman, Andrew Henderson:
LCIA Formatter. 3392 - John M. Volk, Justin Huntington, Richard G. Allen, Forrest Melton, Martha C. Anderson, Ayse Kilic:
flux-data-qaqc: A Python Package for Energy Balance Closure and Post-Processing of Eddy Flux Data. 3418 - Andreas Philippi, Simone Buttler, Nikolai Stein:
ddop: A python package for data-driven operations management. 3429 - Matthew Vaneseltine:
Nominally: A Name Parser for Record Linkage. 3440 - Pasquale Buonomo:
fishRman: A Shiny R Dashboard improving Global Fishing Watch data availability. 3467 - Tobias C. Wood, Emil Ljungberg, Florian Wiesinger:
Radial Interstices Enable Speedy Low-volume Imaging. 3500 - Michael Berks, Geoff J. M. Parker, Ross Little, Sue Cheung:
Madym: A C++ toolkit for quantitative DCE-MRI analysis. 3523 - Giovanni Charles, Sean Wu:
individual: An R package for individual-based epidemiological models. 3539 - Valeria Blesius, Andreas Dominik:
RHRT: An R package to assess Heart Rate Turbulence. 3540 - Shawn T. O'Neil:
TidyTensor: Utilities for multidimensional arrays as named hierarchical structures. 3543 - Frederik Gjørup, Mathias Mørch, Mogens Christensen:
Reel1.0 - A visualization tool for evaluating powder diffraction refinements. 3546 - Albert Weichselbraun:
Inscriptis - A Python-based HTML to text conversion library optimized for knowledge extraction from the Web. 3557 - Mike Smith, James Downs:
ParticleTracker: a gui based particle tracking software. 3611 - Jack Cushman, Matthew Dahl, Michael Lissner:
eyecite: A tool for parsing legal citations. 3617 - Markus Fleschutz, Michael D. Murphy:
elmada: Dynamic electricity carbon emission factors and prices for Europe. 3625 - Thomas Grandits:
A Fast Iterative Method Python package. 3641 - Nicolas Pucino, David Kennedy, Daniel Ierodiaconou:
sandpyper: A Python package for UAV-SfM beach volumetric and behavioural analysis. 3666 - Elizabeth Dupre, Taylor Salo, Zaki Ahmed, Peter A. Bandettini, Katherine L. Bottenhorn, César Caballero-Gaudes, Logan Dowdle, Javier Gonzalez-Castillo, Stephan Heunis, Prantik Kundu, Angela R. Laird, Ross D. Markello, Christopher J. Markiewicz, Stefano Moia, Isla Staden, Joshua Teves, Eneko Uruñuela, Maryam Vaziri-Pashkam, Kirstie J. Whitaker, Daniel A. Handwerker:
TE-dependent analysis of multi-echo fMRI with tedana. 3669 - Alexander Kramer, Yatish Turakhia, Russell Corbett-Detig:
ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees. 3677 - Alexis Hill, James Rybarski, Kuang Hu, Ilya Finkelstein, Claus O. Wilke:
Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets. 3678 - Ariane Sasso, Jost Morgenstern, Felix Musmann, Bert Arnrich:
Devicely: A Python package for reading, timeshifting and writing sensor data. 3679 - Anders Andreasen:
HydDown: A Python package for calculation of hydrogen (or other gas) pressure vessel filling and discharge. 3695 - Robert Richer, Arne Küderle, Martin Ullrich, Nicolas Rohleder, Björn M. Eskofier:
BioPsyKit: A Python package for the analysis of biopsychological data. 3702 - Ejike Ugba:
serp: An R package for smoothing in ordinal regression. 3705 - Félix Chénier:
Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics. 3714 - Arne Tillmann, Anton Thielmann, Gillian Kant, Christoph Weisser, Benjamin Säfken, Alexander Silbersdorff, Thomas Kneib:
AuDoLab: Automatic document labelling and classification for extremely unbalanced data. 3719 - Tin Lai:
sbp-env: A Python Package for Sampling-based Motion Planner and Samplers. 3782
Volume 6, Number 67, November 2021
- Albert Meroño-Peñuela, Carlos Martinez-Ortiz:
grlc: the git repository linked data API constructor. 2731 - Koen Derks, Jacques de Swart, Eric-Jan Wagenmakers, Jan Wille, Ruud Wetzels:
JASP for Audit: Bayesian Tools for the Auditing Practice. 2733 - Vincent Berenz, Maximilien Naveau, Felix Widmaier, Manuel Wüthrich, Jean-Claude Passy, Simon Guist, Dieter Büchler:
The o80 C++ templated toolbox: Designing customized Python APIs for synchronizing realtime processes. 2752 - Platon Karpov, Iskandar Sitdikov, Chengkun Huang, Chris Fryer:
Sapsan: Framework for Supernovae Turbulence Modeling with Machine Learning. 3199 - Donald Williams:
GGMnonreg: Non-Regularized Gaussian Graphical Models in R. 3308 - Lluís Sancho, Juan José Lozano, Azucena Salas:
experDesign: stratifying samples into batches with minimal bias. 3358 - Luis M. Antunes:
CellPyLib: A Python Library for working with Cellular Automata. 3608 - Michaël Touati:
ESVM: an open-source finite volume Electrostatic Vlasov-Maxwell code. 3618 - Brian Savage:
sacio: A library for Seismic Analysis Code data files. 3619 - Vinícius Salazar, João Cavalcante, Daniel de Oliveira, Fabiano L. Thompson, Marta Mattoso:
BioProv - A provenance library for bioinformatics workflows. 3622 - Martin Wilson:
spant: An R package for magnetic resonance spectroscopy analysis. 3646 - Jörg Buchwald, Olaf Kolditz, Thomas Nagel:
ogs6py and VTUinterface: streamlining OpenGeoSys workflows in Python. 3673 - Eugeny A. Metelkin:
Heta compiler: a software tool for the development of large-scale QSP models and compilation into simulation formats. 3708 - Athul Girija, Sarag Saikia, James Longuski, James A. Cutts:
AMAT: A Python package for rapid conceptual design of aerocapture and atmospheric Entry, Descent, and Landing (EDL) missions in a Jupyter environment. 3710 - Joris Paret, Daniele Coslovich:
partycls: A Python package for structural clustering. 3723 - Corentin Nelias:
CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis. 3733 - Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader:
A flexible search system for high-accuracy identification of biological entities and molecules. 3756 - Amanda L. Baxter, Segev Y. BenZvi, Joahan Jaimes, Alexis Coleiro, Marta Molla, Damien Dornic, Spencer Griswold, Tomer Goldhagen, Anne Graf, Alec Habig, Remington Hill, Shunsaku Horiuchi, James P. Kneller, Mathieu Lamoureux, Rafael F. Lang, Massimiliano Lincetto, Jost Migenda, McKenzie Myers, Evan O'Connor, Andrew Renshaw, Kate Scholberg, Andrey Sheshukov, Jeff Tseng, Christopher D. Tunnell, Navya Uberoi, Arkin Worlikar:
SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals. 3772 - Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft, Richard A. Neher:
Nextclade: clade assignment, mutation calling and quality control for viral genomes. 3773 - Enric Grau-Luque, Fabien Atlan, Ignacio Becerril-Romero, Alejandro Pérez-Rodríguez, Maxim Guc, Victor Izquierdo-Roca:
spectrapepper: A Python toolbox for advanced analysis of spectroscopic data for materials and devices. 3781 - Andrea Zonca, Ben Thorne, Nicoletta Krachmalnicoff, Julian Borrill:
The Python Sky Model 3 software. 3783 - Michael Seltenreich:
EDO.js: A comprehensive JavaScript library for interaction with musical set theory in any tuning. 3784 - Andreas Alfons:
robustHD: An R package for robust regression with high-dimensional data. 3786 - Johannes Titz, Markus Burkhardt:
cofad: An R package and shiny app for contrast analysis. 3822 - Richard Teague, Charles Law, Jane Huang, Feilong Meng:
disksurf: Extracting the 3D Structure of Protoplanetary Disks. 3827 - Kevin S. Bonham, Annelle Kayisire, Anika Luo, Vanja Klepac-Ceraj:
Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data. 3876 - Jeffrey R. Stevens:
excluder: An R package that checks for exclusion criteria in online data. 3893 - Diego Hernangómez:
cffr: Generate Citation File Format Metadata for R Packages. 3900
Volume 6, Number 68, December 2021
- Ian Nesbitt, Richard Boaz, Justin Long:
rsudp: A Python package for real-time seismic monitoring with Raspberry Shake instruments. 2565 - Adam Amara, Lucia de la Bella, Simon Birrer, Sarah Bridle, Juan Cordero, Ginevra Favole, Ian Harrison, Ian Harry, William G. Hartley, Coleman Krawczyk, Andrew Lundgren, Brian Nord, Laura Nuttall, Richard Rollins, Philipp Sudek, Sut-Ieng Tam, Nicolas Tessore, Arthur Tolley, Keiichi Umetsu, Andrew Williamson, Laura Wolz:
SkyPy: A package for modelling the Universe. 3056 - Matthew D. Parno, Andrew D. Davis, Linus Seelinger:
MUQ: The MIT Uncertainty Quantification Library. 3076 - Virgile Baudrot, Sandrine Charles:
morse: an R-package to analyse toxicity test data. 3200 - Andy H. Wilkins, Christopher P. Green, Logan H. Harbour, Robert Podgorney:
The MOOSE geochemistry module. 3314 - Arthur Voronin, Alexander Schug:
pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics. 3325 - Ziying Yang, Gosia Mikolajczak, Andrew Turpin:
ConTEXT Explorer: a web-based text analysis tool for exploring and visualizing concepts across time. 3347 - Yu-Te Wu, Yin-Jyun Luo, Tsung-Ping Chen, I-Chieh Wei, Jui-Yang Hsu, Yi-Chin Chuang, Li Su:
Omnizart: A General Toolbox for Automatic Music Transcription. 3391 - Jukka-Pekka Onnela, Caleb Dixon, Keary Griffin, Tucker Jaenicke, Leila Minowada, Sean Esterkin, Alvin Siu, Josh Zagorsky, Eli Jones:
Beiwe: A data collection platform for high-throughput digital phenotyping. 3417 - Klevis Aliaj, Heath B. Henninger:
Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion. 3490 - Eetu Mäkelä, Pihla Toivanen:
Finnish Media Scrapers. 3504 - Rémi Rampin, Vicky Rampin:
Taguette: open-source qualitative data analysis. 3522 - Thomas Hegghammer:
daiR: an R package for OCR with Google Document AI. 3538 - Wolfgang Traylor:
MMM: A C++ library for simulating large herbivores. 3631 - Pablo Tierz, Vyron Christodoulou, John Stevenson, Susan Loughlin:
PyVOLCANS: A Python package to flexibly explore similarities and differences between volcanic systems. 3649 - Nathan Martindale, Scott Stewart:
TX$^2$: Transformer eXplainability and eXploration. 3652 - Dewey Dunnington, Jaimie Harbin, Dan E. Kelley, Clark Richards:
argodata: An R interface to oceanographic data from the International Argo Program. 3659 - Qibang Liu, X. J. Xin:
PDLSM-FEM: Solver of Coupled Peridynamics Least Squares Minimization with Finite Element Method. 3668 - Michael Grudic, Alexander Gurvich:
pytreegrav: A fast Python gravity solver. 3675 - Tomas Andrade, Llibert Salo, Josu C. Aurrekoetxea, Jamie Bamber, Katy Clough, Robin Croft, Eloy de Jong, Amelia Drew, Alejandro Duran, Pedro Ferreira, Pau Figueras, Hal Finkel, Tiago Frana, Bo-Xuan Ge, Chenxia Gu, Thomas Helfer, Juha Jäykkä, Cristian Joana, Markus Kunesch, Kacper Kornet, Eugene Lim, Francesco Muia, Zainab Nazari, Miren Radia, Justin Ripley, Paul Shellard, Ulrich Sperhake, Dina Traykova, Saran Tunyasuvunakool, Zipeng Wang, James Widdicombe, Kaze Wong:
GRChombo: An adaptable numerical relativity code for fundamental physics. 3703 - Timon Emken:
obscura: A modular C++ tool and library for the direct detection of (sub-GeV) dark matter via nuclear and electron recoils. 3725 - Pak Li, Andrew Cunningham, Brandt Gaches, Richard I. Klein, Mark R. Krumholz, Aaron T. Lee, Christopher McKee, Stella S. R. Offner, Anna L. Rosen, Aaron Skinner:
ORION2: A magnetohydrodynamics code for star formation. 3771 - Maximilian Hesselbarth:
shar: An R package to analyze species-habitat associations using point pattern analysis. 3811 - James Chapman, Hao-Ting Wang:
CCA-Zoo: A collection of Regularized, Deep Learning based, Kernel, and Probabilistic CCA methods in a scikit-learn style framework. 3823 - Aisouda Hoshiyar:
ordPens: An R package for Selection, Smoothing and Principal Components Analysis for Ordinal Variables. 3828 - Henk C. den Bakker, Lee S. Katz:
Sepia, a taxonomy oriented read classifier in Rust. 3839 - Charles H. C. Pilgrim:
piecewise-regression (aka segmented regression) in Python. 3859 - Andre Weiner, Richard Semaan:
flowTorch - a Python library for analysis and reduced-order modeling of fluid flows. 3860 - Tiago Toledo:
sknet: A Python framework for Machine Learning in Complex Networks. 3864 - Fabian Schaipp, Oleg Vlasovets, Christian Müller:
GGLasso - a Python package for General Graphical Lasso computation. 3865 - William Michael Landau:
The jagstargets R package: a reproducible workflow framework for Bayesian data analysis with JAGS. 3877 - Jonathan Rittmo, Robert D. McIntosh:
singcar: Comparing single cases to small samples in R. 3887 - Jackson Brown, To Huynh, Isaac Na, Brian Ledbetter, Hawk Ticehurst, Sarah Liu, Emily Gilles, Katlyn Greene, Sung Cho, Shak Ragoler, Nicholas Weber:
Council Data Project: Software for Municipal Data Collection, Analysis, and Publication. 3904 - Shailesh Kumar:
CR-Sparse: Hardware accelerated functional algorithms for sparse signal processing in Python using JAX. 3917 - Mathieu Bernard, Hadrien Titeux:
Phonemizer: Text to Phones Transcription for Multiple Languages in Python. 3958
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