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ORCIDJournal of Open Source Software, Volume 5
Volume 5, Number 45, January 2020
- Kai Alexander von Szadkowski, Simon Reichel
:
Phobos: A tool for creating complex robot models. 1326 - Lukasz Kaczmarczyk, Zahur Ullah, Karol Lewandowski, Xuan Meng, Xiao-Yi Zhou, Ignatios Athanasiadis, Hoang Nguyen, Christophe-Alexandre Chalons-Mouriesse, Euan Richardson, Euan Miur, Andrei G. Shvarts, Mebratu Wakeni, Chris J. Pearce:
MoFEM: An open source, parallel finite element library. 1441 - Wenyang Lyu, Shibabrat Naik, Stephen Wiggins:
UPOsHam: A Python package for computing unstable periodic orbits in two-degree-of-freedom Hamiltonian systems. 1684 - Albert Steppi, Benjamin M. Gyori, John A. Bachman:
Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. 1708 - Lukas Geiger, Plumerai Team:
Larq: An Open-Source Library for Training Binarized Neural Networks. 1746 - Stephan Stock, Jonas Kemmer:
AliasFinder: A Python script to search for the true planetary frequency within radial velocity data. 1771 - Madicken Munk, Matthew J. Turk:
widgyts: Custom Jupyter Widgets for Interactive Data Exploration with yt. 1774 - Taylor B. Arnold, Lauren Tilton:
Distant Viewing Toolkit: A Python Package for the Analysis of Visual Culture. 1800 - Vítor S. Ramos:
SIHR: a MATLAB/GNU Octave toolbox for single image highlight removal. 1822 - Walter Torres, K. C. Bierlich:
MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna. 1825 - Stefano Bianchi:
fathon: A Python package for a fast computation of detrendend fluctuation analysis and related algorithms. 1828 - Jens Mortensen, Morten Gjerding, Kristian Thygesen:
MyQueue: Task and workflow scheduling system. 1844 - Swathi Sheshadri, Benjamin Dann, Timo Hueser, Hansjörg Scherberger:
3D reconstruction toolbox for behavior tracked with multiple cameras. 1849 - Benoît Combès:
miet: an R package for region of interest analysis from magnetic reasonance images. 1862 - Edward J. Oughton, Tom Russell:
cdcam: Cambridge Digital Communications Assessment Model. 1911 - Leonardo Uieda, Santiago Soler, Rémi Rampin, Hugo van Kemenade, Matthew J. Turk, Daniel Shapero, Anderson Banihirwe, John R. Leeman:
Pooch: A friend to fetch your data files. 1943 - Magnus Rahm, Paul Erhart:
WulffPack: A Python package for Wulff constructions. 1944 - Raul Laasner, Xiaochen Du, Aditya Tanikanti, Connor Clayton, Marco Govoni, Giulia Galli, Matti Ropo, Volker Blum:
MatD^3^: A Database and Online Presentation Package for Research Data Supporting Materials Discovery, Design, and Dissemination. 1945 - Roman Feldbauer, Thomas Rattei, Arthur Flexer:
scikit-hubness: Hubness Reduction and Approximate Neighbor Search. 1957 - Matheus Bernardelli de Moraes, André Leon S. Gradvohl:
MOAFS: A Massive Online Analysis library for feature selection in data streams. 1970 - Torben Tvedebrink, Mikkel Meyer Andersen, James Curran:
DNAtools: Tools for Analysing Forensic Genetic DNA Data. 1981 - Héloïse F. Stevance, J. J. Eldridge, Elizabeth Stanway:
Hoki: Making BPASS accessible through Python. 1987 - Michael Hartmann, Gert-Ludwig Ingold:
CaPS: Casimir Effect in the Plane-Sphere Geometry. 2011 - Auriel M. V. Fournier, Matthew Boone, Forrest R. Stevens, Emilio Bruna:
refsplitr: Author name disambiguation, author georeferencing, and mapping of coauthorship networks with Web of Science data. 2028 - Dominic J. Bennett, Hannes Hettling, Daniele Silvestro, Rutger A. Vos, Alexandre Antonelli:
outsider: Install and run programs, outside of R, inside of R. 2038
Volume 5, Number 46, February 2020
- Fidji Berio, Yann Bayle:
Scyland3D: Processing 3D landmarks. 1262 - Matthew K. Lau, Thomas F. J.-M. Pasquier, Margo I. Seltzer:
Rclean: A Tool for Writing Cleaner, More Transparent Code. 1312 - Jérémie Deray, Joan Solà:
Manif: A micro Lie theory library for state estimation in robotics applications. 1371 - Jatinder Sandhu, Anant Girdhar, Rakesh Ramakrishnan, R. D. Teja, Santanu Ghosh:
FEST-3D: Finite-volume Explicit STructured 3-Dimensional solver. 1555 - Diego Kiedanski, Daniel Kofman, José Horta:
PyMarket - A simple library for simulating markets in Python. 1591 - Sangkeun Lee, Jian Peng, Andrew Williams, Dongwon Shin:
ASCENDS: Advanced data SCiENce toolkit for Non-Data Scientists. 1656 - Kamran Javid:
Geometric nested sampling: sampling from distributions defined on non-trivial geometries. 1809 - Akash Nag:
MDL Suite: A language, generator and compiler for describing mazes. 1815 - Joshua Day, Hua Zhou:
OnlineStats.jl: A Julia package for statistics on data streams. 1816 - Jordan H. Creed, Travis A. Gerke, Anders Berglund:
MatSurv: Survival analysis and visualization in MATLAB. 1830 - Stuart Mumford, Nabil Freij, Steven Christe, Jack Ireland, Florian Mayer, V. Keith Hughitt, Albert J. Shih, Daniel Ryan, Simon Liedtke, David Pérez-Suárez, Pritish Chakraborty, Vishnunarayan K, Andrew Inglis, Punyaslok Pattnaik, Brigitta M. Sipocz, Rishabh Sharma, Andrew Leonard, David Stansby, Russell J. Hewett, Alex Hamilton, Laura Hayes, Asish Panda, Matt Earnshaw, Nitin Choudhary, Ankit Kumar, Prateek Chanda, Md. Akramul Haque, Michael Kirk, Michael Mueller, Sudarshan Konge, Rajul Srivastava, Yash Jain, Samuel Bennett, Ankit Baruah, Will T. Barnes, Michael Charlton, Shane A. Maloney, Nicky Chorley, Himanshu, Sanskar Modi, James Mason, Jose Rozo, Larry Manley, Agneet Chatterjee, John Evans, Michael Malocha, Monica G. Bobra, Sourav Ghosh, Dominik Stanczak, Ruben De Visscher, Shresth Verma, Ankit Agrawal, Dumindu Buddhika, Swapnil Sharma, Jongyeob Park, Matt Bates, Dhruv Goel, Garrison Taylor, Goran Cetusic, Jacob, Mateo Inchaurrandieta, Sally Dacie, Sanjeev Dubey, Deepankar Sharma, Erik Bray, Jai Rideout, Serge Zahniy, Tomas Meszaros, Abhigyan Bose, André Chicrala, Ankit, Chloé Guennou, Daniel D'avella, Daniel Williams, Jordan Ballew, Nick Murphy, Priyank Lodha, Thomas Robitaille, Yash Krishan, Andrew Hill, Arthur Eigenbrot, Benjamin Mampaey, Bernhard Wiedemann, Carlos Molina, Duygu Keskek, Ishtyaq Habib, Joseph Letts, Juanjo Bazán, Quinn Arbolante, Reid Gomillion, Yash Kothari, Yash Sharma, Abigail Stevens, Adrian M. Price-Whelan, Ambar Mehrotra, Arseniy Kustov, Brandon Stone, Trung Dang, Emmanuel Arias, Fionnlagh Dover, Freek Verstringe, Gulshan Kumar, Harsh Mathur, Igor Babuschkin, Jaylen Wimbish, Juan Buitrago-Casas, Kalpesh Krishna, Kaustubh Hiware, Manas Mangaonkar, Matthew Mendero, Mickaël Schoentgen, Norbert Gyenge, Ole Streicher, Rajasekhar Mekala, Rishabh Mishra, Shashank Srikanth, Sarthak Jain, Tannmay Yadav, Tessa Wilkinson, Tiago Pereira, Yudhik Agrawal, Jamescalixto, Yasintoda, Sophie Murray:
SunPy: A Python package for Solar Physics. 1832 - Giuseppe Morello, Antonio Claret, Marine Martin-Lagarde, Christophe Cossou, Angelos Tsiara, Pierre-Olivier Lagage:
ExoTETHyS: Tools for Exoplanetary Transits around host stars. 1834 - Mauricio Vargas:
Economiccomplexity: Computational Methods for Economic Complexity. 1866 - Johannes Titz:
passt: An R implementation of the Probability Associator Time (PASS-T) model. 1900 - Kipngeno Kirui, Alois Pichler, Georg Pflug:
ScenTrees.jl: A Julia Package for Generating Scenario Trees and Scenario Lattices for Multistage Stochastic Programming. 1912 - Feiyu Chen, David Sondak, Pavlos Protopapas, Marios Mattheakis, Shuheng Liu, Devansh Agarwal, Marco Di Giovanni:
NeuroDiffEq: A Python package for solving differential equations with neural networks. 1931 - David Litwin, Gregory E. Tucker, Katherine R. Barnhart, Ciaran Harman:
GroundwaterDupuitPercolator: A Landlab component for groundwater flow. 1935 - Ayush Kaushal, Lyndon White, Mike Innes, Rohit Kumar:
WordTokenizers.jl: Basic tools for tokenizing natural language in Julia. 1956 - Titipat Achakulvisut, Daniel E. Acuna, Konrad P. Körding:
Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset XML Dataset. 1979 - Tiago Tresoldi:
DAFSA: a Python library for Deterministic Acyclic Finite State Automata. 1986 - Katherine Eaton:
NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases. 1990 - Oliver Schwengers, Torsten Hain, Trinad Chakraborty, Alexander Goesmann:
ReferenceSeeker: rapid determination of appropriate reference genomes. 1994 - Ellert van der Velden:
CMasher: Scientific colormaps for making accessible, informative and 'cmashing' plots. 2004 - Chia Chang, Christopher Körber, André Walker-Loud:
EspressoDB: A scientific database for managing high-performance computing workflows. 2007 - Iago Lemos, Antonio Lima, Marcus Duarte:
thresholdmodeling: A Python package for modeling excesses over a threshold using the Peak-Over-Threshold Method and the Generalized Pareto Distribution. 2013 - Shalin Shah, Abhishek Kumar Dubey, John H. Reif:
ExTemp: A computational and image-processing suite for extracting temporal barcodes. 2026
Volume 5, Number 46, February 2019
- Nikolai Sellereite, Martin Jullum:
shapr: An R-package for explaining machine learning models with dependence-aware Shapley values. 2027
Volume 5, Number 46, February 2020
- Tyler K. Chafin:
FGTpartitioner: A rapid method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets. 2030 - Andrew Annex, Ben Pearson, Benoît Seignovert, Brian Carcich, Helge Eichhorn, Jesse Mapel, Johan von Forstner, Jonathan McAuliffe, Jorge del Rio, Kristin Berry, K.-Michael Aye, Marcel Stefko, Miguel de Val-Borro, Shankar Kulumani, Shinya Murakami:
SpiceyPy: a Pythonic Wrapper for the SPICE Toolkit. 2050 - Nathan Lyons, James Albert, Nicole Gasparini:
SpeciesEvolver: A Landlab component to evolve life in simulated landscapes. 2066 - Aaron Wolen, Chris Hartgerink, Ryan Hafen, Brian Richards, Courtney Soderberg, Timothy York:
osfr: An R Interface to the Open Science Framework. 2071 - Pascal Stark, Lorenz K. Müller:
COLNA: A Python Package to Analyze Complex, Linear Networks. 2073 - Philippe Boileau, Nima S. Hejazi, Sandrine Dudoit:
scPCA: A toolbox for sparse contrastive principal component analysis in R. 2079
Volume 5, Number 47, March 2020
- Madhavun Candadai, Eduardo J. Izquierdo:
infotheory: A C++/Python package for multivariate information theoretic analysis. 1609 - Jonas Radtke, Guilherme Bertoldo, Carlos Marchi:
DEPP - Differential Evolution Parallel Program. 1701 - Thomas Pak, Ruth E. Baker, Joe Pitt-Francis:
Pakman: a modular, efficient and portable tool for approximate Bayesian inference. 1716 - John Mansour, Julian Giordani, Louis Moresi, Romain Beucher, Owen Kaluza, Mirko Velic, Rebecca Farrington, Steve Quenette, Adam Beall:
Underworld2: Python Geodynamics Modelling for Desktop, HPC and Cloud. 1797 - Fergus R. Cooper, Ruth E. Baker, Miguel O. Bernabeu, Rafel Bordas, Louise Bowler, Alfonso Bueno-Orovio, Helen M. Byrne, Valentina Carapella, Louie Cardone-Noott, Jonathan Cooper, Sara Dutta, Benjamin D. Evans, Alexander G. Fletcher, James A. Grogan, Wenxian Guo, Daniel G. Harvey, Maurice Hendrix, David Kay, Jochen Kursawe, Philip K. Maini, Beth McMillan, Gary R. Mirams, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, Martin Robinson, Blanca Rodríguez, Raymond J. Spiteri, David Gavaghan:
Chaste: Cancer, Heart and Soft Tissue Environment. 1848 - Stefanie Lumnitz, Daniel Arribas-Bel, Renan Xavier Cortes, James D. Gaboardi, Verena C. Griess, Wei Kang, Taylor Oshan, Levi John Wolf, Sergio J. Rey:
splot - visual analytics for spatial statistics. 1882 - Jiaxin Wang, Tess Jaffe, Torsten A. Ensslin, Joe Taylor:
hammurabi X: a C++ package for simulating Galactic emissions. 1889 - Christopher Desjardins, Okan Bulut:
profileR: An R package for profile analysis. 1941 - Mainak Jas, Titipat Achakulvisut, Aid Idrizovic, Daniel E. Acuna, Matthew Antalek, Vinícius Marques, Tommy Odland, Ravi Garg, Mayank Agrawal, Yu Umegaki, Peter Foley, Hugo Fernandes, Drew Harris, Beibin Li, Olivier Pieters, Scott Otterson, Giovanni De Toni, Chris C. Rodgers, Eva L. Dyer, Matti S. Hämäläinen, Konrad P. Körding, Pavan Ramkumar:
Pyglmnet: Python implementation of elastic-net regularized generalized linear models. 1959 - Phyllipe Lima, Eduardo Guerra, Paulo Meirelles:
Annotation Sniffer: A tool to Extract Code Annotations Metrics. 1960 - Andrew J. Quinn, Mark Hymers:
SAILS: Spectral Analysis In Linear Systems. 1982 - Mojtaba Sedigh Fazli, Marcus Hill, Andrew Durden, Rachel Mattson, Allyson T. Loy, Barbara Reaves, Abigail Courtney, Frederick D. Quinn, Chakra Chennubhotla, Shannon Quinn:
OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks. 1983 - Malcolm Barrett, Joshua Millstein:
partition: A fast and flexible framework for data reduction in R. 1991 - Andrew Bennett, Joseph Hamman, Bart Nijssen:
MetSim: A Python package for estimation and disaggregation of meteorological data. 2042 - Andy Nowacki:
SeisModels.jl: A Julia package for models of the Earth's interior. 2043 - Aoife Hughes, Richard J. Morris, Melissa Tomkins:
PyEscape: A narrow escape problem simulator package for Python. 2072 - Sohrab Towfighi:
pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search. 2074 - Matthew Moretz, Daniel Foster, John Weber, Rinty Chowdhury, Shah Rafique, Evan B. Goldstein, Somya D. Mohanty:
psi-collect: A Python module for post-storm image collection and cataloging. 2075 - Alan F. Rubin:
fqfa: A pure Python package for genomic sequence files. 2076 - Courtney Smith, Tristan Salles, Ana Vila-Concejo:
RADWave: Python code for ocean surface wave analysis by satellite radar altimeter. 2083 - Sunghyun Kim, Samantha Hood, Puck van Gerwen, Lucy D. Whalley, Aron Walsh:
CarrierCapture.jl: Anharmonic Carrier Capture. 2102 - Brett M. Morris:
fleck: Fast approximate light curves for starspot rotational modulation. 2103 - Roni Choudhury, Muratahan Aykol, Samuel Gratzl, Joseph Montoya, Jens S. Hummelshøj:
MaterialNet: A web-based graph explorer for materials science data. 2105 - Phil Snyder, Meghasyam Tummalacherla, Thanneer Malai Perumal, Larsson Omberg:
mhealthtools: A Modular R Package for Extracting Features from Mobile and Wearable Sensor Data. 2106 - Giovanni Birolo, Andrea Telatin:
covtobed: a simple and fast tool to extract coverage tracks from BAM files. 2119 - Samuel R. Hinton, Dillon Brout:
Pippin: A pipeline for supernova cosmology. 2122 - He Ma, Marco Govoni, Giulia Galli:
PyZFS: A Python package for first-principles calculations of zero-field splitting tensors. 2160
Volume 5, Number 48, April 2020
- Tom Eulenfeld:
rf: Receiver function calculation in seismology. 1808 - Shalin Shah:
JCOL: A Java package for solving the graph coloring problem. 1843 - Simon O'meara, Shuxuan Xu, David Topping, Gerard Capes, Douglas Lowe, M. Rami Alfarra, Gordon McFiggans:
PyCHAM: CHemistry with Aerosol Microphysics in Python. 1918 - Nicolas Karasiak:
Museo ToolBox: A Python library for remote sensing including a new way to handle rasters. 1978 - Thomas Helfer, Jérémy Bleyer, Tero Frondelius, Ivan Yashchuk, Thomas Nagel, Dmitri Naumov:
The MFrontGenericInterfaceSupport project. 2003 - Joshua W. Steer, Oliver Stocks, Jack Parsons, Peter R. Worsley, Alexander S. Dickinson:
ampscan: A lightweight Python package for shape analysis of prosthetics and orthotics. 2060 - J. Sebastian Paez, Michael Wendt, Nadia Lanman:
scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data. 2061 - Guilherme P. Castelão:
A Framework to Quality Control Oceanographic Data. 2063 - Raphael Timbó, Rodrigo Martins, Gabriel Bachmann, Flavio Rangel, Júlia Mota, Juliana Valério, Thiago G. Ritto:
ROSS - Rotordynamic Open Source Software. 2120 - Maximilian Rabe, Shravan Vasishth, Sven Hohenstein, Reinhold Kliegl, Daniel J. Schad:
hypr: An R package for hypothesis-driven contrast coding. 2134 - Simon Brugman, Ian Eaves:
Visions: An Open-Source Library for Semantic Data. 2145 - Travis Hesketh:
pygen-structures: A Python package to generate 3D molecular structures for simulations using the CHARMM forcefield. 2157 - David Zwicker:
py-pde: A Python package for solving partial differential equations. 2158 - Minnie Joo, Nicolás Schmidt, Sergio Béjar, Vineeta Yadav, Bumba Mukherjee:
BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events. 2164 - Henry Wilde, Vincent A. Knight, Jonathan W. Gillard:
Matching: A Python library for solving matching games. 2169 - Steffen Herbold:
Autorank: A Python package for automated ranking of classifiers. 2173
Volume 5, Number 49, May 2020
- David Torres Sanchez:
cspy: A Python package with a collection of algorithms for the (Resource) Constrained Shortest Path problem. 1655 - Kacper Sokol, Alexander Hepburn, Rafael Poyiadzi, Matthew Clifford, Raúl Santos-Rodríguez, Peter A. Flach:
FAT Forensics: A Python Toolbox for Implementing and Deploying Fairness, Accountability and Transparency Algorithms in Predictive Systems. 1904 - Kiret Dhindsa, Oliver Cook, Thomas Mudway, Areeb Khawaja, Ron Harwood, Ranil Sonnadara:
LFSpy: A Python Implementation of Local Feature Selection for Data Classification with scikit-learn Compatibility. 1958 - Yuriy Babin:
Recan: Python tool for analysis of recombination events in viral genomes. 2014 - Jason Cory Brunson:
ggalluvial: Layered Grammar for Alluvial Plots. 2017 - Ryan P. McGehee, Dennis C. Flanagan, Puneet Srivastava:
WEPPCLIFF: A command-line tool to process climate inputs for soil loss models. 2029 - Nicolas Renaud, Cunliang Geng:
The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries. 2077 - Peter M. C. Harrison:
psychTestR: An R package for designing and conducting behavioural psychological experiments. 2088 - Nora Eisner, Chris J. Lintott, Suzanne Aigrain:
LATTE: Lightcurve Analysis Tool for Transiting Exoplanets. 2101 - Brian de Silva, Kathleen P. Champion, Markus Quade, Jean-Christophe Loiseau, J. Nathan Kutz, Steven L. Brunton:
PySINDy: A Python package for the sparse identification of nonlinear dynamical systems from data. 2104 - Johannes Titz:
mimosa: A Modern Graphical User Interface for 2-level Mixed Models. 2116 - Francesco Witte, Ilja Tuschy:
TESPy: Thermal Engineering Systems in Python. 2178 - Andrew Van Benschoten, Austin Ouyang, Francisco Bischoff, Tyler Marrs:
MPA: a novel cross-language API for time series analysis. 2179
Volume 5, Number 50, June 2020
- Samuel Letellier-Duchesne, Louis Leroy:
archetypal: A Python package for collecting, simulating, converting and analyzing building archetypes. 1833 - Kaashif Hymabaccus, Dmitrii V. Pasechnik:
RepnDecomp: A GAP package for decomposing linear representations of finite groups. 1835 - Silvana Ayala Pelaez, Chris Deline:
bifacial_radiance: a python package for modeling bifacial solar photovoltaic systems. 1865 - David Meyer, Robert Schoetter, Valéry Masson,