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Journal of Open Source Software, Volume 4
Volume 4, Number 33, 2019
- Fei Xiang
, Bethany L. Dearlove
, Simon D. W. Frost:
genieR: An R package for inference of demographic history of phylogenies. 634 - Kyle D. Peterson
, Aaron R. Caldwell
:
mbir: Magnitude-Based Inferences. 746 - Alexander LeNail
:
NN-SVG: Publication-Ready Neural Network Architecture Schematics. 747 - Antoine Muller
, Charles Pontonnier
, Pierre Puchaud
, Georges Dumont
:
CusToM: a Matlab toolbox for musculoskeletal simulation. 927 - Daniel Hatton
:
eights: BS 8888: 2011 first angle projection drawings from FreeCAD 3D model. 974 - Matias Carrasco Kind
, Alex Drlica-Wagner
, Audrey Koziol
, Donald Petravick
:
easyaccess: Enhanced SQL command line interpreter for astronomical surveys. 1022 - Vaishnav Tadiparthi
, Shao-Chen Hsu
, Raktim Bhattacharya
:
STEDY: Software for TEnsegrity DYnamics. 1042 - Padraig T. Looney, Gordon N. Stevenson
, Sally L. Collins
:
3D ultrasound file reading and coordinate transformations. 1063 - Eric T. Dawson
, Richard Durbin
:
GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats. 1083 - Matthew J. Gidden
, Daniel Huppmann
:
pyam: a Python Package for the Analysis and Visualization of Models of the Interaction of Climate, Human, and Environmental Systems. 1095 - Erica Christensen
, Glenda Yenni
, Hao Ye
, Juniper Simonis
, Ellen Bledsoe
, Renata Diaz
, Shawn D. Taylor
, Ethan P. White
, S. K. Morgan Ernest
:
portalr: an R package for summarizing and using the Portal Project Data. 1098 - Morten Lund
, John Rasmussen
, Michael Skipper Andersen
:
AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. 1108 - Zijie Zhao
, Maxime Marin
:
A MATLAB toolbox to detect and analyze marine heatwaves. 1124 - Pieter Gijsbers
, Joaquin Vanschoren
:
GAMA: Genetic Automated Machine learning Assistant. 1132 - David Meyer
, Didier Thevenard
:
PsychroLib: a library of psychrometric functions to calculate thermodynamic properties of air. 1137 - Blaise Thompson
, Kyle Sunden
, Darien Morrow
, Daniel Kohler
, John Wright
:
WrightTools: a Python package for multidimensional spectroscopy. 1141 - Ravin Kumar
, Colin Carroll
, Ari Hartikainen
, Osvaldo A. Martin
:
ArviZ a unified library for exploratory analysis of Bayesian models in Python. 1143 - Ryan Hagenson
:
swsc: A sitewise UCE partitioner. 1146 - Pingjun Chen
, Lin Yang:
tissueloc: Whole slide digital pathology image tissue localization. 1148 - Alexander Fabisch
:
pytransform3d: 3D Transformations for Python. 1159 - Michael C. Heiber
:
KMC\_Lattice v2.0: An Object-Oriented C\texttt{++} Library for Custom Kinetic Monte Carlo Simulations. 1168 - Robin Lovelace
, Malcolm Morgan
, Layik Hama
, Mark Padgham
:
stats19: A package for working with open road crash data. 1181 - Jasper Ho
, Garway Ng, Mathias Renaud
, Art F. Y. Poon:
sierra-local: A lightweight standalone application for drug resistance prediction. 1186 - Kel N. Markert
:
cartoee: Publication quality maps using Earth Engine. 1207
Volume 4, Number 34, February 2019
- Felix Ospald
:
fibergen: An introductory tool for FFT-based material homogenization. 1027 - Sebastian Meyer
:
polyCub: An R package for Integration over Polygons. 1056 - Patricia Wollstadt
, Joseph T. Lizier
, Raul Vicente
, Conor Finn
, Mario Martínez-Zarzuela
, Pedro A. M. Mediano
, Leonardo Novelli
, Michael Wibral
:
IDTxl: The Information Dynamics Toolkit xl: a Python package for the efficient analysis of multivariate information dynamics in networks. 1081 - Pieter Eendebak
, Alan R. Vazquez
:
OApackage: A Python package for generation and analysis of orthogonal arrays, optimal designs and conference designs. 1097 - Vincent Magnin
, James Tappin
, Jens Hunger
, Jerry De Lisle:
gtk-fortran: a GTK+ binding to build Graphical User Interfaces in Fortran. 1109 - Iacopo Garizio
:
Py-school-match: Matching algorithms to assign students to schools. 1111 - Jonathan Schnabel
:
PyMS: Python for Mycorrhizal Symbiosis data analysis. 1125 - Brett M. Morris
, Trevor Dorn-Wallenstein
, Emily Levesque
, Charli Sakari
, Doug Gies
, Katherine Lester
, Yuta Notsu
, Allison Youngblood
, Russet McMillan:
arcesetc: ARC Echelle Spectrograph Exposure Time Calculator. 1130 - Thu-Hien To
, Stephen M. Pederson
:
strandCheckR: An R package for quantifying and removing double strand sequences for strand-specific RNA-seq. 1145 - August Guang:
RSeqAn: Headers and wrappers for the SeqAn library in R. 1160 - Sivaram Ambikasaran
, Karan Singh, Shyam Sankaran:
HODLRlib: A Library for Hierarchical Matrices. 1167 - Gáspár Lukács
:
CITapp - a response time-based Concealed Information Test lie detector web application. 1179 - Robert Meolic
:
The Biddy BDD package. 1189 - Andreas Baum
, Laurent Vermue
:
Multiblock PLS: Block dependent prediction modeling for Python. 1190 - Kenneth R. Lyons
, Benjamin W. L. Margolis
:
AxoPy: A Python Library for Implementing Human-Computer Interface Experiments. 1191 - Andrew T. Jones, Jessica Bagnall, Hien Duy Nguyen
:
BoltzMM: an R package for maximum pseudolikelihood estimation of fully-visible Boltzmann machines. 1193 - Mahmoud Gadalla
, Marco Tezzele
, Andrea Mola
, Gianluigi Rozza
:
BladeX: Python Blade Morphing. 1203 - Adam Symington
, Joshua Tse
, Marco Molinari
, Arnaud Marmier
, Stephen C. Parker
:
surfinpy: A Surface Phase Diagram Generator. 1210 - Philipp S. Sommer
, Dilan Rech
, Manuel Chevalier
, Basil Davis
:
straditize: Digitizing stratigraphic diagrams. 1216 - Richard Teague
:
eddy: Extracting Protoplanetary Disk Dynamics with Python. 1220 - Tommaso Leonardi
:
Bedparse: feature extraction from BED files. 1228 - Adrien Leger
, Tommaso Leonardi
:
pycoQC, interactive quality control for Oxford Nanopore Sequencing. 1236 - Benjamin Wilson
:
HyperNaut: a navigator for the hyperbolic plane. 1240 - Michael Notter
, Dan Gale
, Peer Herholz
, Ross D. Markello
, Marie-Laure Bielser
, Kirstie J. Whitaker
:
AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images. 1257 - Sam Abbott
:
getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data. 1260 - Alice Harpole
, Michael Zingale
, Ian Hawke
, Taher Chegini
:
pyro: a framework for hydrodynamics explorations and prototyping. 1265 - Mikkel Meyer Andersen
:
mitolina: MITOchondrial LINeage Analysis. 1266 - Carl Boettiger
:
Ecological Metadata as Linked Data. 1276 - Eric E. Brown
:
tacmagic: Positron emission tomography analysis in R. 1281 - Evan Munson
, Christopher Smith
, Bradley C. Boehmke, Jason K. Freels
:
Sentiment Analysis of Twitter Data (saotd). 764
Volume 4, Number 35, 2019
- Allison A. Throm
, Anthony A. French
:
CytobankAPIstats: Computes Signaling and Population Statistics for Cytometry Data on Cytobank using 'CytobankAPI'. 445 - Matthew D. Harris
:
KLRfome - Kernel Logistic Regression on Focal Mean Embeddings. 722 - Viktor Polak
, Yuezhang Zhu
, Sung Bae
, Jason Motha
, Brendon Bradley
, Hoby Razafindrakoto
:
GMSimViz: Automated 3D Visualization of Ground Motion Simulation with Generic Mapping Tools (GMT). 808 - Henrik A. Kjeldsberg
, Aslak Wigdahl Bergersen
, Kristian Valen-Sendstad
:
morphMan: Automated manipulation of vascular geometries. 1065 - Benjamin Bengfort
, Rebecca Bilbro
:
Yellowbrick: Visualizing the Scikit-Learn Model Selection Process. 1075 - Alexandros-Stavros Iliopoulos
, Abhishek Kumar Dubey
, Xiaobai Sun:
idvf: Iterative Inversion of Deformation Vector Field with Adaptive Bi-residual Feedback Control. 1076 - Steve Davis
:
vcftoolz: a Python package for comparing and evaluating Variant Call Format files. 1144 - George Datseris
, Joel Hobson:
MIDI.jl: Simple and intuitive handling of MIDI data. 1166 - Bernhard Fröhler
, Johannes Weissenböck
, Marcel Schiwarth
, Johann Kastner
, Christoph Heinzl
:
open_iA: A tool for processing and visual analysis of industrial computed tomography datasets. 1185 - Victoria L. Rubin
, Chris Brogly
, Nadia Conroy
, Yimin Chen
, Sarah Cornwell
, Toluwase Victor Asubiaro
:
A News Verification Browser for the Detection of Clickbait, Satire, and Falsified News. 1208 - Georgina L. Wellock
, Benjamin J. Morgan
:
pyscses: a PYthon Space-Charge Site-Explicit Solver. 1209 - John D. Garrett
, Ghassan Yassin:
QMix: A Python package for simulating the quasiparticle tunneling currents in SIS junctions. 1231 - Tormod Landet
:
Ocellaris: a DG FEM solver for free-surface flows. 1239 - Scott P. Kolodziej
, Mohsen Aznaveh
, Matthew Bullock, Jarrett David
, Timothy A. Davis
, Matthew Henderson, Yifan Hu
, Read Sandström
:
The SuiteSparse Matrix Collection Website Interface. 1244 - Romain Thomas
:
dfitspy: a dfits|fitsort implementation in python. 1249 - Amir M. Mir
, Jalal A. Nasiri
:
LightTwinSVM: A Simple and Fast Implementation of Standard Twin Support Vector Machine Classifier. 1252 - Alexander J. Gates
, Yong-Yeol Ahn
:
CluSim: a python package for calculating clustering similarity. 1264 - Emily C. Zabor
:
riskclustr: Functions to Study Etiologic Heterogeneity. 1269 - Christian Holz
, Eric Kemp-Benedict
, Tom Athanasiou, Sivan Kartha
:
The Climate Equity Reference Calculator. 1273 - Changcheng Li
:
JuliaCall: an R package for seamless integration between R and Julia. 1284 - Arman Oganisian
:
ChiRP: Chinese Restaurant Process Mixtures for Regression and Clustering. 1287 - Andrea Zonca
, Leo P. Singer, Daniel Lenz
, Martin Reinecke, Cyrille Rosset
, Eric Hivon
, Krzysztof M. Gorski
:
healpy: equal area pixelization and spherical harmonics transforms for data on the sphere in Python. 1298 - Robert A Gilmore
, Shaurita Hutchins
, Xiao Zhang
, Eric J. Vallender
:
MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows. 1299 - Matthew Bartos
, Abhiram Mullapudi
, Sara C. Troutman
:
rrcf: Implementation of the Robust Random Cut Forest algorithm for anomaly detection on streams. 1336 - Ashkbiz Danehkar
:
AtomNeb: IDL Library for Atomic Data of Ionized Nebulae. 898 - Andrew J. Page
, Torsten Seemann:
TipToft: detecting plasmids contained in uncorrected long read sequencing data. 1021
Volume 4, Number 36, 2019
- Michael Stenskjær Christensen
:
Samewords: Automatic word disambigation in critical text editions. 941 - Chad Curtis
, Ariel Rokem
, Elizabeth Nance
:
diff_classifier: Parallelization of multi-particle tracking video analyses. 989 - Sebastian Lamprecht
:
Pyoints: A Python package for point cloud, voxel and raster processing. 990 - Lyndon White
, David Ellison
:
Embeddings.jl: easy access to pretrained word embeddings from Julia. 1013 - Luis Benet
, David P. Sanders
:
TaylorSeries.jl: Taylor expansions in one and several variables in Julia. 1043 - Romain Beucher
, Louis Moresi
, Julian Giordani
, John Mansour
, Dan Sandiford
, Rebecca Farrington
, Luke Mondy
, Claire Mallard
, Patrice Rey
, Guillaume Duclaux
, Owen Kaluza
, Arijit Laik
, Sara Morón
:
UWGeodynamics: A teaching and research tool for numerical geodynamic modelling. 1136 - Ian H. Bell
:
CEGO: C++11 Evolutionary Global Optimization. 1147 - Maxim Terpilovskii
:
scikit-posthocs: Pairwise multiple comparison tests in Python. 1169 - Lucas J. Koerner
:
Instrbuilder: A Python package for electrical instrument control. 1172 - Daniel Leehr
, Mercedes Gosby:
TraitDB: Web application database of phenotypic trait data. 1201 - Andrei Novikov
:
PyClustering: Data Mining Library. 1230 - Gregory R. Lee
, Ralf Gommers
, Filip Wasilewski
, Kai Wohlfahrt
, Aaron O'Leary
:
PyWavelets: A Python package for wavelet analysis. 1237 - Scott Cole
, Thomas Donoghue
, Richard Gao
, Bradley Voytek
:
NeuroDSP: A package for neural digital signal processing. 1272 - Nelle Varoquaux
, Nicolas Servant
:
iced: fast and memory efficient normalization of contact maps. 1286 - Zoe Meers
, Robert Hickman, Thomas J. Leeper
:
ggparliament: A ggplot2 extension for parliament plots in R. 1313 - Ryan R. Wick
:
Badread: simulation of error-prone long reads. 1316 - HyoungAh Kim
, Vito D'Orazio
, Patrick T. Brandt
, Michael Shoemate
, Sayeed Salam
, Latifur Khan
, Jared Looper
:
UTDEventData: An R package to access political event data. 1322 - Moliavko Oleksandr
, Drozdovskyi Taras
, Petrychenko Vitalii
, Oleg Yu. Kopysov
:
uJVM: Lightweight Java Virtual Machine for embedded systems. 1338 - Mikael Mortensen
, Lisandro Dalcín
, David E. Keyes
:
mpi4py-fft: Parallel Fast Fourier Transforms with MPI for Python. 1340 - Matthieu Ancellin
, Frédéric Dias
:
Capytaine: a Python-based linear potential flow solver. 1341 - Franz-Sebastian Krah
, Christoph Heibl
:
rGUIDANCE - alignment confidence score computation in R. 1350 - Shawn Banasick
:
KADE: A desktop application for Q methodology. 1360 - Rutger A. Vos
, Nnadi Nnaemeka Emmanuel, John Chinyere Aguiyi:
WGS2NCBI - Toolkit for preparing genomes for submission to NCBI. 1364
Volume 4, Number 37, 2019
- Maria Florencia D'Andrea
, Julie Celine Brodeur
:
shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment. 785 - David Kinkead
, Deborah Brown
, Peter Ellerton
, Claudio Mazzola
:
Reasons: A digital argument mapping library for modern browsers. 1044 - Jason Neal
, Pedro Figueira
:
Eniric: Extended NIR Information Content. 1053 - Aaron Carter-Enyi
:
EMViz (Early Music Visualization): MATLAB runtime application. 1094 - Jon Hill
:
HRDS: A Python package for hierarchical raster datasets. 1112 - Justin A. Alsing
:
dlmmc: Dynamical linear model regression for atmospheric time-series analysis. 1157 - Christopher Prener
, Charlie Revord:
areal: An R package for areal weighted interpolation. 1221 - Freek Stulp
, Gennaro Raiola
:
DmpBbo: A versatile Python/C++ library for Function Approximation, Dynamical Movement Primitives, and Black-Box Optimization. 1225 - Adam Lanman
, Bryna J. Hazelton
, Danny Jacobs
, Matthew Kolopanis
, Jonathan C. Pober
, James E. Aguirre
, Nithyanandan Thyagarajan
:
pyuvsim: A comprehensive simulation package for radio interferometers in python. 1234 - Stefan Johann van der Walt
, Arien Crellin-Quick
, Joshua S. Bloom
:
SkyPortal: An Astronomical Data Platform. 1247 - Mingze He
, Kokulapalan Wimalanathan
, Peng Liu
, Carolyn J. Lawrence-Dill
:
Compare Expression Profiles for Pre-defined Gene Groups with C-REx. 1255 - Casper O. da Costa-Luis
:
tqdm: A Fast, Extensible Progress Meter for Python and CLI. 1277 - Nelson A. Roque
, Nilam Ram
:
tsfeaturex: An R Package for Automating Time Series Feature Extraction. 1279 - Philip D. Waggoner
, Ryan Kennedy, Scott Clifford:
Detecting Fraud in Online Surveys by Tracing, Scoring, and Visualizing IP Addresses. 1285 - Jeff T. Gostick
, Zohaib Atiq Khan
, Thomas G. Tranter
, Mathew D. R. Kok
, Mehrez Agnaou
, Mohamm Adamin Sadeghi
, Rhodri Jervis
:
PoreSpy: A Python Toolkit for Quantitative Analysis of Porous Media Images. 1296 - Mika Hämäläinen
:
UralicNLP: An NLP Library for Uralic Languages. 1345