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ORCIDJournal of Open Source Software, Volume 1
Volume 1, Number 1, 2016
- Gilles Louppe
, Kyle Cranmer, Juan Pavez:
carl: a likelihood-free inference toolbox. 11 - Jake VanderPlas:
mst_clustering: Clustering via Euclidean Minimum Spanning Trees. 12 - Alice Harpole, Ian Hawke:
R3D2: Relativistic Reactive Riemann problem solver for Deflagrations and Detonations. 16 - Zhao Zhang, Daniel S. Katz, André Merzky, Matteo Turilli, Shantenu Jha, Yadu Nand Babuji:
Application Skeleton: Generating Synthetic Applications for Infrastructure Research. 17 - Matthew J. Wakefield:
Xenomapper: Mapping reads in a mixed species context. 18 - Peter F. Hickey:
Representation and Manipulation of Genomic Tuples in R. 20 - James K. Tauber:
pyuca: a Python implementation of the Unicode Collation Algorithm. 21 - James P. Balhoff:
Scowl: a Scala DSL for programming with the OWL API. 23
Volume 1, Number 2, 2016
- Daniel Foreman-Mackey:
corner.py: Scatterplot matrices in Python. 24 - Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas A. Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. Williams, Pjotr Prins:
GeneNetwork: framework for web-based genetics. 25 - Conrad Sanderson, Ryan R. Curtin:
Armadillo: a template-based C++ library for linear algebra. 26 - Simon J. Greenhill:
Phylogemetric: A Python library for calculating phylogenetic network metrics. 28 - Christian T. Jacobs, Alexandros Avdis:
Git-RDM: A research data management plugin for the Git version control system. 29
Volume 1, Number 3, 2016
- Christopher R. Madan:
Prism: Multiple spline regression with regularization, dimensionality reduction, and feature selection. 31 - Nitin Madnani, Anastassia Loukina:
RSMTool: collection of tools building and evaluating automated scoring models. 33 - Michael A. Levy:
gwdegree: Improving interpretation of geometrically-weighted degree estimates in exponential random graph models. 36 - Julia Silge, David Robinson:
tidytext: Text Mining and Analysis Using Tidy Data Principles in R. 37 - Simon D. W. Frost:
Gillespie.jl: Stochastic Simulation Algorithm in Julia. 42
Volume 1, Number 4, 2016
- Zoran Cuckovic:
Advanced viewshed analysis: a Quantum GIS plug-in for the analysis of visual landscapes. 32 - Simon Bogutzky, Jan Christoph Schrader, Nassrin Hajinejad, Barbara Grüter:
PsychoPhysioCollector: A Smartphone-Based Data Collection App for Psychophysiological Research. 40 - Christopher D. Cooper, Natalia C. Clementi, Gilbert Forsyth, Lorena A. Barba:
PyGBe: Python, GPUs and Boundary elements for biomolecular electrostatics. 43 - Samuel R. Hinton:
ChainConsumer. 45 - Claudia Vitolo, Andrew Russell, Allan Tucker:
rdefra: Interact with the UK AIR Pollution Database from DEFRA. 51 - Timothée Giraud, Nicolas Lambert:
cartography: Create and Integrate Maps in your R Workflow. 54
Volume 1, Number 5, 2016
- C. Titus Brown, Luiz Irber:
sourmash: a library for MinHash sketching of DNA. 27 - Robert T. McGibbon, Carlos X. Hernández, Matthew P. Harrigan, Steven Kearnes, Mohammad M. Sultan, Stanislaw Jastrzebski, Brooke E. Husic, Vijay S. Pande:
Osprey: Hyperparameter Optimization for Machine Learning. 34 - Simon Bogutzky, Phillip Marsch, Licínio Roque, Nassrin Hajinejad, Barbara Grüter:
PsychoPhysioPipeline: A Processing and Analysis Pipeline for Psychophysiological Research. 41 - Dirk Eddelbuettel, Wush Wu:
RcppCNPy: Read-Write Support for NumPy Files in R. 55 - Jonathan A. Michaels, Hansjörg Scherberger:
hebbRNN: A Reward-Modulated Hebbian Learning Rule for Recurrent Neural Networks. 60 - Dean A. Attali:
ezknitr: Avoid the Typical Working Directory Pain When Using 'knitr'. 75 - Paul G. Constantine, Ryan Howard, Andrew G. Salinger, Zachary Grey, Paul Diaz, Leslie Fletcher:
Python Active-subspaces Utility Library. 79
Volume 1, Number 6, 2016
- Eetu Mäkelä:
LAS: an integrated language analysis tool for multiple languages. 35 - Sebastian Bocquet, Faustin W. Carter:
pygtc: beautiful parameter covariance plots (aka. Giant Triangle Confusograms). 46 - Kyle Barbary:
SEP: Source Extractor as a library. 58 - Carl Ganz:
rintrojs: A Wrapper for the Intro.js Library. 63 - Andrew J. Page, Sascha Steinbiss, Ben Taylor, Torsten Seemann, Jacqueline A. Keane:
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL. 80 - Christos Theodoropoulos, Nikolaos Skoulikidis, Anastasios Stamou:
Habfuzz: A tool to calculate the instream hydraulic habitat suitability using fuzzy logic and fuzzy Bayesian inference. 82 - Manuel Holtgrewe, Dieter Beule:
VCFPy: a Python 3 library with good support for both reading and writing VCF. 85 - Danny Arends, Yang Li, Gudrun A. Brockmann, Ritsert C. Jansen, Robert W. Williams, Pjotr Prins:
Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype. 87 - Zachary M. Jones, Fridolin Linder:
edarf: Exploratory Data Analysis using Random Forests. 92
Volume 1, Number 7, 2016
- Matt Germonprez, Thomas Gurney, Sai Uday Shankar Korlimarla, Robin A. Gandhi:
DoSOCS: A System for SPDX 2.0 Document Creation and Storage. 38 - Guillermo Hernández, Francisco Fernández:
xpecgen: A program to calculate x-ray spectra generated in tungsten anodes. 62 - Philipp H. Boersch-Supan:
rucrdtw: Fast time series subsequence search in R. 100 - Sean M. Hughes:
plater: Read, Tidy, and Display Data from Microtiter Plates. 106 - René L. Warren:
RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences. 116
Volume 1, Number 8, 2016
- Markus Raab:
Elektra: universal framework to access configuration parameters. 44 - Nicholas M. Van Horn, Aaron Beveridge:
MassMine: Your Access To Data. 50 - Claudia Vitolo, Peter Wells, Martin Dobias, Wouter Buytaert:
fuse: An R package for ensemble Hydrological Modelling. 52 - Rodrigo V. Honorato:
CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database. 53 - Julien Ponge, Yannick Loiseau, Frédéric Le Mouël, Nicolas Stouls, Philippe Charrière, Daniel Petisme, Sylvain Desgrais, Franck Verrot:
Eclipse Golo. 93 - Kevin DeSimone, Ariel Rokem, Keith Schneider:
popeye: a population receptive field estimation tool. 103 - Rémi Rampin, Fernando Chirigati, Dennis E. Shasha, Juliana Freire, Vicky Steeves:
ReproZip: The Reproducibility Packer. 107 - Matthew J. Wakefield:
SurvivalVolume: interactive volume threshold survival graphs. 111 - Andrew J. Page, Ben Taylor, Jacqueline A. Keane:
Multilocus sequence typing by blast from de novo assemblies against PubMLST. 118 - Seward Lee:
finreportr: Financial Data from U.S. Securities and Exchange Commission. 119 - Brian McFee:
resampy: efficient sample rate conversion in Python. 125 - Jeff Goldsmith:
vbvs.concurrent: Fitting Methods for the Functional Linear Concurrent Model. 141
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