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Journal 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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