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ORCIDJournal of Open Source Software, Volume 2
Volume 2, Number 9, 2017
- Claudia Vitolo
:
hddtools: Hydrological Data Discovery Tools. 56 - Kelly A. Kearney:
ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm. 64 - Andrew Halterman:
Mordecai: Full Text Geoparsing and Event Geocoding. 91 - Jonathan D. Herman, Will Usher:
SALib: An open-source Python library for Sensitivity Analysis. 97 - Clayton Norris, Philip A. Schrodt, John Beieler:
PETRARCH2: Another Event Coding Program. 133 - Benjamin Naecker, Niru Maheswaranathan, Surya Ganguli, Stephen Baccus:
Pyret: A Python package for analysis of neurophysiology data. 137 - Kristian Jensen, João G. R. Cardoso, Nikolaus Sonnenschein:
Optlang: An algebraic modeling language for mathematical optimization. 139 - Camille Scott:
shmlast: An improved implementation of Conditional Reciprocal Best Hits with LAST and Python. 142 - Eduardo S. M. Alexandre:
Limarka: making possible Brazilian students writing dissertation and thesis with Markdown. 169
Volume 2, Number 10, 2017
- Michel Lang, Bernd Bischl, Dirk Surmann:
batchtools: Tools for R to work on batch systems. 135 - Bryna J. Hazelton, Daniel C. Jacobs, Jonathan C. Pober, Adam P. Beardsley:
pyuvdata: an interface for astronomical interferometeric datasets in python. 140 - Matthew McCormick, Mark L. Palmeri, Jean-Christophe Fillion-Robin, Stephen R. Aylward:
SlicerITKUltrasound: A 3D Slicer extension for scan conversion of B-mode and next-generation ultrasound imaging modalities. 153 - Devarshi Ghoshal, Valerie C. Hendrix, William Fox, Sowmya Balasubhramanian, Lavanya Ramakrishnan:
FRIEDA: Flexible Robust Intelligent Elastic Data Management Framework. 164 - R. Daniel Kortschak, Josh Bleecher Snyder, Manolis Maragkakis, David L. Adelson:
bíogo: a simple high-performance bioinformatics toolkit for the Go language. 167 - R. Daniel Kortschak, Brent S. Pedersen, David L. Adelson:
bíogo/hts: high throughput sequence handling for the Go language. 168 - Bradley C. Boehmke, Robert T. Montgomery, Jeffrey A. Ogden, Jason K. Freels:
KraljicMatrix: An R package for implementing the Kraljic Matrix to strategically analyze a firm's purchasing portfolio. 170 - David Ardia, Kris Boudt, Jean-Philippe Gagnon-Fleury:
RiskPortfolios: Computation of Risk-Based Portfolios in R. 171 - David Ardia, Keven Bluteau:
nse: Computation of Numerical Standard Errors in R. 172 - Anthony Caravaggi:
remBoot: An R package for Random Encounter Modelling. 176 - Adam H. Sparks, Tomislav Hengl, Andrew Nelson:
GSODR: Global Summary Daily Weather Data in R. 177
Volume 2, Number 11, 2017
- Andy Yu Zhu Yao, David Kane:
walkr: MCMC Sampling from Non-Negative Convex Polytopes. 61 - Pranay Seshadri, Geoffrey T. Parks:
Effective-Quadratures (EQ): Polynomials for Computational Engineering Studies. 166 - Julia Niskanen, Elina Salmela, Hannes Lohi:
AncesTrim - a tool for trimming complex pedigrees. 179 - Miguel de Val-Borro, Martin A. Cordiner, Stefanie N. Milam, Steven B. Charnley:
Cine: Line excitation by infrared fluorescence in cometary atmospheres. 182 - Stuart W. D. Grieve:
spatial-efd: A spatial-aware implementation of elliptical Fourier analysis. 189 - Charles Crabtree, Michael J. Nelson:
Plotrr: Functions for making visual exploratory data analysis with nested data easier. 190 - Scott Chamberlain, Jeffrey W. Hollister:
lawn: An R client for the Turf Javascript Library for Geospatial Analysis. 194 - Matti Pastell:
Weave.jl: Scientific Reports Using Julia. 204 - Leland McInnes, John Healy, Steve Astels:
hdbscan: Hierarchical density based clustering. 205 - Joshua Higgins, Violeta Holmes, Colin C. Venters:
VCC: A framework for building containerized reproducible cluster software environments. 208 - Chapman Siu:
Ramble: Parser Combinator for R. 209
Volume 2, Number 12, 2017
- Nicolas CARPi, Alexander Minges, Matthieu Piel:
eLabFTW: An open source laboratory notebook for research labs. 146 - Carlos X. Hernández, Matthew P. Harrigan, Mohammad M. Sultan, Vijay S. Pande:
MSMExplorer: Data Visualizations for Biomolecular Dynamics. 188 - Nicholas Cortale, Dylan E. McNamara:
skedm: Empirical Dynamic Modeling. 207 - Geoff Boeing:
OSMnx: A Python package to work with graph-theoretic OpenStreetMap street networks. 215 - Adam H. Sparks:
getCRUCLdata: Use and Explore CRU CL v. 2.0 Climatology Elements in R. 230 - Christopher Lucien Mutel:
Brightway: An open source framework for Life Cycle Assessment. 236 - Sven N. Willner, Corinne Hartin, Robert Gieseke:
pyhector: A Python interface for the simple climate model Hector. 248
Volume 2, Number 13, 2017
- Kolby L. Weisenburger, Joseph Huehnerhoff, Emily M. Levesque, Philip Massey:
acronym: An Automatic Reduction Pipeline for Astronomical Images. 102 - Antti Kamppi, Esko Pekkarinen, Janne Virtanen, Joni-Matti Määttä, Juho Järvinen, Lauri Matilainen, Mikko Teuho, Timo D. Hämäläinen:
Kactus2: A graphical EDA tool built on the IP-XACT standard. 151 - Bradley C. Boehmke, Jason K. Freels:
learningCurve: An implementation of Crawford's and Wright's learning curve production functions. 202 - Luca Romano:
YoungTab. 221 - Davide Gerosa, Michele Vallisneri:
filltex: Automatic queries to ADS and INSPIRE databases to fill LaTex bibliography. 222 - Marie E. Rognes, Patrick E. Farrell, Simon W. Funke, Johan E. Hake, Mary M. Maleckar:
cbcbeat: an adjoint-enabled framework for computational cardiac electrophysiology. 224 - Abhinav Tushar, Nicholas G. Reich:
flusight: interactive visualizations for infectious disease forecasts. 231 - Kevin D. Murray, Justin O. Borevitz:
libqcpp: A C++14 sequence quality control library. 232 - Andrew J. Page, Martin Hunt, Torsten Seemann, Jacqueline A. Keane:
SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. 243 - Christopher Lucien Mutel:
Pandarus: GIS toolkit for regionalized life cycle assessment. 244 - Benjamin J. Morgan:
lattice_mc: A Python Lattice-Gas Monte Carlo Module. 247 - Gaute Hope:
IBCAO_py: A matplotlib library for using the International Bathymetric Chart of the Arctic Ocean with cartopy and matplotlib. 250 - James P. Howard II:
Virtual Bumblebees Artificial Life Simulation. 256 - Andreas Mayer:
Noisyopt: A Python library for optimizing noisy functions. 258 - Roger A. Light:
Mosquitto: server and client implementation of the MQTT protocol. 265
Volume 2, Number 14, 2017
- Sean M. Anderson, Bernardo S. Mendoza:
SHGYield. 242 - John P. Didion:
xphyle: Extraordinarily simple file handling. 255 - Rory Nolan, Sergi Padilla-Parra:
filesstrings: An R package for file and string manipulation. 260 - Sebastian Raschka:
BioPandas: Working with molecular structures in pandas DataFrames. 279 - Bennett Kleinberg, Maximilian Mozes:
Web-based text anonymization with Node.js: Introducing NETANOS (Named entity-based Text Anonymization for Open Science). 293 - Taylor B. Arnold:
kerasR: R Interface to the Keras Deep Learning Library. 296 - Mark Padgham, Robin Lovelace, Maëlle Salmon, Bob Rudis:
osmdata. 305
Volume 2, Number 15, 2017
- Dominik Moritz:
Text detection in screen images with a Convolutional Neural Network. 235 - Daniel S. Standage, Ali yari, Lisa J. Cohen, Michael R. Crusoe, Tim Head, Luiz Irber, Shannon E. K. Joslin, N. B. Kingsley, Kevin D. Murray, Russell Y. Neches, Camille Scott, Ryan Shean, Sascha Steinbiss, Cait Sydney, C. Titus Brown:
khmer release v2.1: software for biological sequence analysis. 272 - Alexander Bock, Emil Axelsson, Karl Bladin, Jonathas Costa, Gene Payne, Matthew Territo, Joakim Kilby, Masha Kuznetsova, Carter Emmart, Anders Ynnerman:
OpenSpace: An open-source astrovisualization framework. 281 - Bede Constantinides, David L. Robertson:
Kindel: indel-aware consensus for nucleotide sequence alignments. 282 - Daniele De Vecchi, Fabio Dell'Acqua, Daniel Aurelio Galeazzo:
CLOOPSy - Copernicus Land cOver crOwdsourcing Platform for Sentinel-based mapping. 291 - Nima S. Hejazi, Weixin Cai, Alan E. Hubbard:
biotmle: Targeted Learning for Biomarker Discovery. 295 - Anush Krishnan, Olivier Mesnard, Lorena A. Barba:
cuIBM: a GPU-based immersed boundary method code. 301
Volume 2, Number 16, 2017
- Paul Francis Harrison:
Varistran: Anscombe's variance stabilizing transformation for RNA-seq gene expression data. 257 - Danny Hermes:
Helper for Bézier Curves, Triangles, and Higher Order Objects. 267 - Pi-Yueh Chuang, Lorena A. Barba:
AmgXWrapper: An interface between PETSc and the NVIDIA AmgX library. 280 - Lucas A. Wilson, John M. Fonner, Jason Allison, Oscar Esteban, Harry Kenya, Marshall Lerner:
Launcher: A simple tool for executing high throughput computing workloads. 289 - Edmund Noel Dawe, Piti Ongmongkolkul, Giordon Stark:
root_numpy: The interface between ROOT and NumPy. 307 - Simon J. van Heeringen:
genomepy: download genomes the easy way. 320 - Konstantin Stadler:
The country converter coco - a Python package for converting country names between different classification schemes. 332 - Maëlle Salmon, Sreekanth Vakacherla, Carles Milà, Julian D. Marshall, Cathryn Tonne:
rtimicropem: an R package supporting the analysis of RTI MicroPEM output files. 333 - Mathew W. McLean:
RefManageR: Import and Manage BibTeX and BibLaTeX References in R. 338 - P. James Joyce:
Lcopt - An interactive tool for creating fully parameterised Life Cycle Assessment (LCA) foreground models. 339 - Francesco Strozzi, Raoul Jean Pierre Bonnal:
Pipengine: an ultra light YAML-based pipeline execution engine. 341 - Juanjo Bazán, Oscar Gonzalez-Recio:
Nimbus: a Ruby gem to implement Random Forest algorithms in a genomic selection context. 351 - Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon:
'Sequana': a Set of Snakemake NGS pipelines. 352 - Sebastiano Ferraris, Dzhoshkun Ismail Shakir, Johannes L. van der Merwe, Willy Gsell, Jan Deprest, Tom Vercauteren:
Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format. 354 - Nicholas J. Tierney:
visdat: Visualising Whole Data Frames. 355 - Alicia N. Schep, Sarah K. Kummerfeld:
iheatmapr: Interactive complex heatmaps in R. 359 - Philipp S. Sommer:
The psyplot interactive visualization framework. 363 - Tanner C. Hobson, Mathieu Doucet, Ricardo M. Ferraz Leal:
Django Remote Submission. 366 - Benjamin J. Morgan:
bsym: A basic symmetry module. 370
Volume 2, Number 17, 2017
- Sepand Haghighi:
Pyrgg: Python Random Graph Generator. 331 - Ashlee N. Ford Versypt, Grace K. Harrell, Alexandra N. McPeak:
ACEInhibPKPD: An open-source MATLAB app for a pharmacokinetic/pharmacodynamic model of ACE inhibition. 340 - Adrian M. Price-Whelan, Daniel Foreman-Mackey:
schwimmbad: A uniform interface to parallel processing pools in Python. 357 - Marco van Hulten:
ComPlot: Comparison Plotter to visually evaluate ocean model simulations. 368 - Sébastien Binet, Bastian Wieck, David Blyth, Emmanuel Busato, Michaël Ughetto, Peter Waller:
Go-HEP: libraries for High Energy Physics analyses in Go. 372 - Shane J. Latham:
array_split: Multi-dimensional array partitioning. 373 - Jakob Bossek:
mcMST: A Toolbox for the Multi-Criteria Minimum Spanning Tree Problem. 374 - Pradeep Reddy Raamana, Stephen C. Strother:
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity. 382 - Benjamin W. L. Margolis:
SimuPy: A Python framework for modeling and simulating dynamical systems. 396 - Travis Kessler, John Hunter Mack:
ECNet: Large scale machine learning projects for fuel property prediction. 401 - Michael J. Kane:
bittrex: An R client for the Bittrex Crypto-Currency Exchange. 402 - Adam H. Sparks, Mark Padgham, Hugh Parsonage, Keith G. Pembleton:
bomrang: Fetch Australian Government Bureau of Meteorology Data in R. 411
Volume 2, Number 18, 2017
- R. Daniel Kortschak, David L. Adelson:
bíogo/ncbi: interfaces to NCBI services for the Go language. 234 - Offray Vladimir Luna Cárdenas:
Grafoscopio: A moldable tool for literate computing and reproducible research. 251 - Thomas Cokelaer, Jürgen Hasch:
'Spectrum': Spectral Analysis in Python. 348 - Marcin Wojdyr:
UglyMol: a WebGL macromolecular viewer focused on the electron density. 350 - Conrad Sanderson, Ryan R. Curtin:
gmm_diag and gmm_full: C++ classes for multi-threaded Gaussian mixture models and Expectation-Maximisation. 365 - Gabriele Rovigatti:
Production Function Estimation in R: The prodest Package. 371 - Sara Mahar, Matthew Bellis:
hmis: A python tool to visualize and analyze HMIS data. 384 - Adrian M. Price-Whelan:
Gala: A Python package for galactic dynamics. 388 - Ben Lauwens:
ResumableFunctions: C# sharp style generators for Julia. 400 - Philip Stegmaier, Alexander E. Kel, Edgar Wingender:
geneXplainR: An R interface for the geneXplain platform. 412 - Tim Folsom, V. P. Nagraj:
hei: Calculate Healthy Eating Index (HEI) Scores. 417 - Bérénice A. Batut, Björn A. Grüning:
ENASearch: A Python library for interacting with ENA's API. 418 - Andrew C. Heusser, Paxton C. Fitzpatrick, Campbell E. Field, Kirsten Ziman, Jeremy R. Manning:
Quail: A Python toolbox for analyzing and plotting free recall data. 424 - Vanessa V. Sochat:
Singularity Registry: Open Source Registry for Singularity Images. 426
Volume 2, Number 19, 2017
- Kivan Polimis, Ariel Rokem, Bryna J. Hazelton:
Confidence Intervals for Random Forests in Python. 124 - Dominique Makowski, Léo Dutriaux:
Neuropsydia.py: A Python Module for Creating Experiments, Tasks and Questionnaires. 259 - Natalia C. Clementi, Gilbert Forsyth, Christopher D. Cooper, Lorena A. Barba:
PyGBe-LSPR: Python and GPU Boundary-integral solver for electrostatics. 306 - Pradeep Reddy Raamana, Stephen C. Strother:
Histogram-weighted Networks for Feature Extraction, Connectivity and Advanced Analysis in Neuroscience. 380 - Yuxuan Zhang, Jean Bilheux:
ImagingReso: A Tool for Neutron Resonance Imaging. 407 - Andrew P. Smith:
UKCensusAPI: python and R interfaces to the nomisweb UK census data API. 408 - Haytham M. Fayek:
MatDL: A Lightweight Deep Learning Library in MATLAB. 413 - Carlos X. Hernández, Vijay S. Pande:
MDEntropy: Information-Theoretic Analyses for Molecular Dynamics. 427 - José Jiménez, Josep Ginebra:
pyGPGO: Bayesian Optimization for Python. 431 - Marcus D. Bloice, Christof Stocker, Andreas Holzinger:
Augmentor: An Image Augmentation Library for Machine Learning. 432 - Philippe Renard:
Hytool: an open source matlab toolbox for the interpretation of hydraulic tests using analytical solutions. 441 - Henry Kironde, Benjamin D. Morris, Akash Goel, Andrew Zhang, Akshay Narasimha, Shivam Negi, David J. Harris, Deborah Gertrude Digges, Kapil Kumar, Amritanshu Jain, Kunal Pal, Kevinkumar Amipara, Prabh Simran Singh Baweja, Ethan P. White:
Retriever: Data Retrieval Tool. 451 - Carl Boettiger:
Generating CodeMeta Metadata for R Packages. 454 - George Datseris:
DynamicalBilliards.jl: An easy-to-use, modular and extendable Julia package for Dynamical Billiard systems in two dimensions. 458
Volume 2, Number 20, 2017
- Andre Schmeißer, Daniel Burkhart, Dominik Linn, Johannes Schnebele, Manuel Ettmüller, Simone Gramsch, Walter Arne:
Ensight4Matlab: read, process, and write files in EnSight® Gold format from C++ or MATLAB®. 217 - Rohan Dandage, Kausik Chakraborty:
dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data. 362 - Ilja Honkonen:
High-Dimensional Integrator. 437 - Olivier Delestre, Frédéric Darboux, François James, Carine Lucas, Christian Laguerre, Stéphane Cordier:
FullSWOF: Full Shallow-Water equations for Overland Flow. 448 - Sachin Chitta, Eitan Marder-Eppstein, Wim Meeussen, Vijay Pradeep, Adolfo Rodríguez Tsouroukdissian, Jonathan Bohren, Dave Coleman, Bence Magyar, Gennaro Raiola, Mathias Lüdtke, Enrique Fernandez Perdomo:
ros_control: A generic and simple control framework for ROS. 456 - Ai Okada, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Yuichi Shiraishi:
A framework for generating interactive reports for cancer genome analysis. 457 - Daniel Suess, Milan Holzäpfel:
mpnum: A matrix product representation library for Python. 465 - Mark Padgham, Richard Ellison:
bikedata. 471 - Stephen R. Lockley, Claudio Benghi, Martin Cerný:
Xbim.Essentials: a library for interoperable building information applications. 473 - David J. Harris:
An easy-to-use p5.js 3D object picker for visual artists. 475 - Sam J. Albers:
tidyhydat: Extract and Tidy Canadian Hydrometric Data. 511 - Sinan Shi, David Pérez-Suárez, Steve K. Harris, Niall S. MacCallum, David Brealey, Mervyn Singer, James Hetherington:
Critical care data processing tools. 513
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