Last update:
Sat Aug 31 12:31:53 MDT 2024
Gilles Louppe and
Kyle Cranmer and
Juan Pavez \pkgcarl: a likelihood-free inference
toolbox . . . . . . . . . . . . . . . . 11:1--11:1
Jake VanderPlas \pkgmst\_clustering: Clustering via
Euclidean Minimum Spanning Trees . . . . 12:1--12:1
Alice Harpole and
Ian Hawke \pkgR3D2: Relativistic Reactive Riemann
problem solver for Deflagrations and
Detonations . . . . . . . . . . . . . . 16:1--16:1
Zhao Zhang and
Daniel S. Katz and
Andre Merzky and
Matteo Turilli and
Shantenu Jha and
Yadu Nand Application Skeleton: Generating
Synthetic Applications for
Infrastructure Research . . . . . . . . 17:1--17:2
Matthew J. Wakefield \pkgXenomapper: Mapping reads in a mixed
species context . . . . . . . . . . . . 18:1--18:1
Peter F. Hickey Representation and Manipulation of
Genomic Tuples in R . . . . . . . . . . 20:1--20:1
J. K. Tauber \pkgpyuca: a Python implementation of
the Unicode Collation Algorithm . . . . 21:1--21:1
James P. Balhoff \pkgScowl: a Scala DSL for programming
with the OWL API . . . . . . . . . . . . 23:1--23:1
Daniel Foreman-Mackey \pkgcorner.py: Scatterplot matrices in
Python . . . . . . . . . . . . . . . . . 24:1--24:2
Zachary Sloan and
Danny Arends and
Karl W. Broman and
Arthur Centeno and
Nicholas Furlotte and
Harm Nijveen and
Lei Yan and
Xiang Zhou and
Robert W. Williams and
Pjotr Prins \pkgGeneNetwork: framework for web-based
genetics . . . . . . . . . . . . . . . . 25:1--25:3
Conrad Sanderson and
Ryan Curtin \pkgArmadillo: a template-based C++
library for linear algebra . . . . . . . 26:1--26:2
Simon J. Greenhill \pkgPhylogemetric: A Python library for
calculating phylogenetic network metrics 28:1--28:1
Christian T. Jacobs and
Alexandros Avdis \pkgGit-RDM: A research data management
plugin for the Git version control
system . . . . . . . . . . . . . . . . . 29:1--29:2
Christopher R. Madan \pkgPrism: Multiple spline regression
with regularization, dimensionality
reduction, and feature selection . . . . 31:1--31:3
Nitin Madnani and
Anastassia Loukina \pkgRSMTool: collection of tools
building and evaluating automated
scoring models . . . . . . . . . . . . . 33:1--33:1
Michael A. Levy \pkggwdegree: Improving interpretation
of geometrically-weighted degree
estimates in exponential random graph
models . . . . . . . . . . . . . . . . . 36:1--36:1
Julia Silge and
David Robinson \pkgtidytext: Text Mining and Analysis
Using Tidy Data Principles in R . . . . 37:1--37:3
Simon D. W. Frost \pkgGillespie.jl: Stochastic Simulation
Algorithm in Julia . . . . . . . . . . . 42:1--42:1
Zoran Cuckovic Advanced viewshed analysis: a Quantum
GIS plug-in for the analysis of visual
landscapes . . . . . . . . . . . . . . . 32:1--32:3
Simon Bogutzky and
Jan Christoph Schrader and
Nassrin Hajinejad and
Barbara Grüter \pkgPsychoPhysioCollector: A
Smartphone-Based Data Collection App for
Psychophysiological Research . . . . . . 40:1--40:3
Christopher D. Cooper and
Natalia C. Clementi and
Gilbert Forsyth and
Lorena A. Barba \pkgPyGBe: Python, GPUs and Boundary
elements for biomolecular electrostatics 43:1--43:1
Samuel Hinton \pkgChainConsumer . . . . . . . . . . . 45:1--45:2
Claudia Vitolo and
Andrew Russell and
Allan Tucker \pkgrdefra: Interact with the UK AIR
Pollution Database from DEFRA . . . . . 51:1--51:2
Timothée Giraud and
Nicolas Lambert \pkgcartography: Create and Integrate
Maps in your R Workflow . . . . . . . . 54:1--54:2
C. Titus Brown and
Luiz Irber \pkgsourmash: a library for MinHash
sketching of DNA . . . . . . . . . . . . 27:1--27:1
Robert T. McGibbon and
Carlos X. Hernández and
Matthew P. Harrigan and
Steven Kearnes and
Mohammad M. Sultan and
Stanis\law Jastrzebski and
Brooke E. Husic and
Vijay S. Pande \pkgOsprey: Hyperparameter Optimization
for Machine Learning . . . . . . . . . . 34:1--34:2
Simon Bogutzky and
Phillip Marsch and
Licínio Roque and
Nassrin Hajinejad and
Barbara Grüter \pkgPsychoPhysioPipeline: A Processing
and Analysis Pipeline for
Psychophysiological Research . . . . . . 41:1--41:3
Dirk Eddelbuettel and
Wush Wu \pkgRcppCNPy: Read-Write Support for
NumPy Files in R . . . . . . . . . . . . 55:1--55:1
Jonathan A. Michaels and
Hansjörg Scherberger \pkghebbRNN: A Reward-Modulated Hebbian
Learning Rule for Recurrent Neural
Networks . . . . . . . . . . . . . . . . 60:1--60:2
Dean Attali \pkgezknitr: Avoid the Typical Working
Directory Pain When Using `\pkgknitr' 75:1--75:1
Paul Constantine and
Ryan Howard and
Andrew Glaws and
Zachary Grey and
Paul Diaz and
Leslie Fletcher \pkgPython Active-subspaces Utility
Library . . . . . . . . . . . . . . . . 79:1--79:1
Eetu Mäkelä \pkgLAS: an integrated language analysis
tool for multiple languages . . . . . . 35:1--35:2
Sebastian Bocquet and
Faustin W. Carter \pkgpygtc: beautiful parameter
covariance plots (aka. Giant Triangle
Confusograms) . . . . . . . . . . . . . 46:1--46:3
Kyle Barbary \pkgSEP: Source Extractor as a library 58:1--58:2
Carl Ganz \pkgrintrojs: A Wrapper for the
\pkgIntro.js Library . . . . . . . . . . 63:1--63:1
Andrew J. Page and
Sascha Steinbiss and
Ben Taylor and
Torsten Seemann and
Jacqueline A. Keane \pkgGFF3toEMBL: Preparing annotated
assemblies for submission to EMBL . . . 80:1--80:1
Christos Theodoropoulos and
Nikolaos Skoulikidis and
Anastasios Stamou \pkgHabfuzz: A tool to calculate the
instream hydraulic habitat suitability
using fuzzy logic and fuzzy Bayesian
inference . . . . . . . . . . . . . . . 82:1--82:2
Manuel Holtgrewe and
Dieter Beule \pkgVCFPy: a Python 3 library with good
support for both reading and writing VCF 85:1--85:1
Danny Arends and
Yang Li and
Gudrun A. Brockmann and
Ritsert C. Jansen and
Robert W. Williams and
Pjotr Prins Correlation Trait Loci (CTL) mapping:
phenotype network inference subject to
genotype . . . . . . . . . . . . . . . . 87:1--87:4
Zachary M. Jones and
Fridolin J. Linder \pkgedarf: Exploratory Data Analysis
using Random Forests . . . . . . . . . . 92:1--92:4
Matt Germonprez and
Thomas Gurney and
Sai Uday Shankar Korlimarla and
Robin Gandhi \pkgDoSOCS: A System for \pkgSPDX 2.0
Document Creation and Storage . . . . . 38:1--38:1
Guillermo Hernández and
Francisco Fernández \pkgxpecgen: A program to calculate
X-ray spectra generated in tungsten
anodes . . . . . . . . . . . . . . . . . 62:1--62:2
Philipp H. Boersch-Supan \pkgrucrdtw: Fast time series
subsequence search in R . . . . . . . . 100:1--100:2
Sean M. Hughes \pkgplater: Read, Tidy, and Display Data
from Microtiter Plates . . . . . . . . . 106:1--106:1
Rene L. Warren \pkgRAILS and \pkgCobbler: Scaffolding
and automated finishing of draft genomes
using long DNA sequences . . . . . . . . 116:1--116:2
Markus Raab \pkgElektra: universal framework to
access configuration parameters . . . . 44:1--44:2
Nicholas M. Van Horn and
Aaron Beveridge \pkgMassMine: Your Access To Data . . . 50:1--50:1
Claudia Vitolo and
Peter Wells and
Martin Dobias and
Wouter Buytaert \pkgfuse: An R package for ensemble
Hydrological Modelling . . . . . . . . . 52:1--52:2
Rodrigo V. Honorato \pkgCAZy-parser a way to extract
information from the Carbohydrate-Active
enZYmes Database . . . . . . . . . . . . 53:1--53:1
Julien Ponge and
Yannick Loiseau and
Frédéric Le Mouël and
Nicolas Stouls and
Philippe Charri\`ere and
Daniel Petisme and
Sylvain Desgrais and
Franck Verrot Eclipse Golo . . . . . . . . . . . . . . 93:1--93:1
Kevin DeSimone and
Ariel Rokem and
Keith Schneider \pkgpopeye: a population receptive field
estimation tool . . . . . . . . . . . . 103:1--103:1
Rémi Rampin and
Fernando Chirigati and
Dennis Shasha and
Juliana Freire and
Vicky Steeves \pkgReproZip: The Reproducibility Packer 107:1--107:3
Matthew J. Wakefield \pkgSurvivalVolume: interactive volume
threshold survival graphs . . . . . . . 111:1--111:2
Andrew J. Page and
Ben Taylor and
Jacqueline A. Keane Multilocus sequence typing by blast from
de novo assemblies against PubMLST . . . 118:1--118:2
Seward Lee \pkgfinreportr: Financial Data from U.S.
Securities and Exchange Commission . . . 119:1--119:1
Brian McFee \pkgresampy: efficient sample rate
conversion in Python . . . . . . . . . . 125:1--125:1
Jeff Goldsmith \pkgvbvs.concurrent: Fitting Methods for
the Functional Linear Concurrent Model 141:1--141:1
Claudia Vitolo \pkghddtools: Hydrological Data
Discovery Tools . . . . . . . . . . . . 56:1--56:2
Kelly A. Kearney \pkgecopath\_matlab: A Matlab-based
implementation of the Ecopath food web
algorithm . . . . . . . . . . . . . . . 64:1--64:2
Andrew Halterman \pkgMordecai: Full Text Geoparsing and
Event Geocoding . . . . . . . . . . . . 91:1--91:1
Jon Herman and
Will Usher \pkgSALib: An open-source Python library
for Sensitivity Analysis . . . . . . . . 97:1--97:2
Clayton Norris and
Philip Schrodt and
John Beieler \pkgPETRARCH2: Another Event Coding
Program . . . . . . . . . . . . . . . . 133:1--133:1
Benjamin Naecker and
Niru Maheswaranathan and
Surya Ganguli and
Stephen Baccus \pkgPyret: A Python package for analysis
of neurophysiology data . . . . . . . . 137:1--137:1
Kristian Jensen and
Joao G. R. Cardoso and
Nikolaus Sonnenschein \pkgOptlang: An algebraic modeling
language for mathematical optimization 139:1--139:1
Camille Scott \pkgshmlast: An improved implementation
of Conditional Reciprocal Best Hits with
LAST and Python . . . . . . . . . . . . 142:1--142:4
Eduardo S. M. Alexandre \pkgLimarka: making possible Brazilian
students writing dissertation and thesis
with Markdown . . . . . . . . . . . . . 169:1--169:1
Michel Lang and
Bernd Bischl and
Dirk Surmann \pkgbatchtools: Tools for R to work on
batch systems . . . . . . . . . . . . . 135:1--135:2
Bryna J. Hazelton and
Daniel C. Jacobs and
Jonathan C. Pober and
Adam P. Beardsley \pkgpyuvdata: an interface for
astronomical interferometeric datasets
in python . . . . . . . . . . . . . . . 140:1--140:1
Matthew M. McCormick and
Mark L. Palmeri and
Jean-Christophe Fillion-Robin and
Stephen Aylward \pkgSlicerITKUltrasound: A $3$D Slicer
extension for scan conversion of B-mode
and next-generation ultrasound imaging
modalities . . . . . . . . . . . . . . . 153:1--153:1
Devarshi Ghoshal and
Valerie Hendrix and
William Fox and
Sowmya Balasubhramanian and
Lavanya Ramakrishnan \pkgFRIEDA: Flexible Robust Intelligent
Elastic Data Management Framework . . . 164:1--164:3
R. Daniel Kortschak and
Josh Bleecher Snyder and
Manolis Maragkakis and
David L. Adelson \pkgbíogo: a simple high-performance
bioinformatics toolkit for the Go
language . . . . . . . . . . . . . . . . 167:1--167:1
R. Daniel Kortschak and
Brent S. Pedersen and
David L. Adelson \pkgbíogo/hts: high throughput sequence
handling for the Go language . . . . . . 168:1--168:1
Bradley C. Boehmke and
Robert T. Montgomery and
Jeffrey A. Ogden and
Jason K. Freels \pkgKraljicMatrix: An R package for
implementing the Kraljic Matrix to
strategically analyze a firm's
purchasing portfolio . . . . . . . . . . 170:1--170:2
David Ardia and
Kris Boudt and
Jean-Philippe Gagnon-Fleury \pkgRiskPortfolios: Computation of
Risk-Based Portfolios in R . . . . . . . 171:1--171:1
David Ardia and
Keven Bluteau \pkgnse: Computation of Numerical
Standard Errors in R . . . . . . . . . . 172:1--172:2
Anthony Caravaggi \pkgremBoot: An R package for Random
Encounter Modelling . . . . . . . . . . 176:1--176:3
Adam H. Sparks and
Tomislav Hengl and
Andrew Nelson \pkgGSODR: Global Summary Daily Weather
Data in R . . . . . . . . . . . . . . . 177:1--177:2
Andy Yu Zhu Yao and
David Kane \pkgwalkr: MCMC Sampling from
Non-Negative Convex Polytopes . . . . . 61:1--61:1
Pranay Seshadri and
Geoffrey Parks \pkgEffective-Quadratures (EQ):
Polynomials for Computational
Engineering Studies . . . . . . . . . . 166:1--166:2
Julia Niskanen and
Elina Salmela and
Hannes Lohi \pkgAncesTrim --- a tool for trimming
complex pedigrees . . . . . . . . . . . 179:1--179:1
Miguel de Val-Borro and
Martin A. Cordiner and
Stefanie N. Milam and
Steven B. Charnley \pkgCine: Line excitation by infrared
fluorescence in cometary atmospheres . . 182:1--182:2
Stuart W. D. Grieve \pkgspatial-efd: A spatial-aware
implementation of elliptical Fourier
analysis . . . . . . . . . . . . . . . . 189:1--189:2
Charles Crabtree and
Michael J. Nelson \pkgPlotrr: Functions for making visual
exploratory data analysis with nested
data easier . . . . . . . . . . . . . . 190:1--190:2
Scott Chamberlain and
Jeffrey W. Hollister \pkglawn: An R client for the Turf
Javascript Library for Geospatial
Analysis . . . . . . . . . . . . . . . . 194:1--194:1
Matti Pastell \pkgWeave.jl: Scientific Reports Using
Julia . . . . . . . . . . . . . . . . . 204:1--204:1
Leland McInnes and
John Healy and
Steve Astels \pkghdbscan: Hierarchical density based
clustering . . . . . . . . . . . . . . . 205:1--205:2
Joshua Higgins and
Violeta Holmes and
Colin Venters \pkgVCC: A framework for building
containerized reproducible cluster
software environments . . . . . . . . . 208:1--208:1
Chapman Siu \pkgRamble: Parser Combinator for R . . 209:1--209:1
Nicolas Carpi and
Alexander Minges and
Matthieu Piel \pkgeLabFTW: An open source laboratory
notebook for research labs . . . . . . . 146:1--146:1
Carlos X. Hernández and
Matthew P. Harrigan and
Mohammad M. Sultan and
Vijay S. Pande \pkgMSMExplorer: Data Visualizations for
Biomolecular Dynamics . . . . . . . . . 188:1--188:2
Nicholas Cortale and
Dylan McNamara \pkgskedm: Empirical Dynamic Modeling 207:1--207:2
Geoff Boeing \pkgOSMnx: A Python package to work with
graph-theoretic OpenStreetMap street
networks . . . . . . . . . . . . . . . . 215:1--215:4
Adam H. Sparks \pkggetCRUCLdata: Use and Explore
\pkgCRU CL v. 2.0 Climatology Elements
in R . . . . . . . . . . . . . . . . . . 230:1--230:1
Chris Mutel \pkgBrightway: An open source framework
for Life Cycle Assessment . . . . . . . 236:1--236:2
Sven N. Willner and
Corinne Hartin and
Robert Gieseke \pkgpyhector: A Python interface for the
simple climate model Hector . . . . . . 248:1--248:2
Kolby L. Weisenburger and
Joseph Huehnerhoff and
Emily M. Levesque and
Philip Massey \pkgacronym: An Automatic Reduction
Pipeline for Astronomical Images . . . . 102:1--102:2
Antti Kamppi and
Esko Pekkarinen and
Janne Virtanen and
Joni-Matti Määttä and
Juho Järvinen and
Lauri Matilainen and
Mikko Teuho and
Timo D. Hämäläinen \pkgKactus2: A graphical EDA tool built
on the IP-XACT standard . . . . . . . . 151:1--151:1
Bradley C. Boehmke and
Jason K. Freels \pkglearningCurve: An implementation of
Crawford's and Wright's learning curve
production functions . . . . . . . . . . 202:1--202:1
Luca Romano \pkgYoungTab . . . . . . . . . . . . . . 221:1--221:1
Davide Gerosa and
Michele Vallisneri \pkgfilltex: Automatic queries to ADS
and INSPIRE databases to fill LaTex
bibliography . . . . . . . . . . . . . . 222:1--222:1
Marie E. Rognes and
Patrick E. Farrell and
Simon W. Funke and
Johan E. Hake and
Molly M. C. Maleckar \pkgcbcbeat: an adjoint-enabled
framework for computational cardiac
electrophysiology . . . . . . . . . . . 224:1--224:1
Abhinav Tushar and
Nicholas G. Reich \pkgflusight: interactive visualizations
for infectious disease forecasts . . . . 231:1--231:2
Kevin D. Murray and
Justin O. Borevitz \pkglibqcpp: A C++14 sequence quality
control library . . . . . . . . . . . . 232:1--232:1
Andrew J. Page and
Martin Hunt and
Torsten Seemann and
Jacqueline A. Keane \pkgSaffronTree: Fast, reference-free
pseudo-phylogenomic trees from reads or
contigs . . . . . . . . . . . . . . . . 243:1--243:2
Chris Mutel \pkgPandarus: GIS toolkit for
regionalized life cycle assessment . . . 244:1--244:1
Benjamin J. Morgan \pkglattice\_mc: A Python Lattice-Gas
Monte Carlo Module . . . . . . . . . . . 247:1--247:2
Gaute Hope \pkgIBCAO\_py: A matplotlib library for
using the International Bathymetric
Chart of the Arctic Ocean with cartopy
and matplotlib . . . . . . . . . . . . . 250:1--250:2
James P. Howard II Virtual Bumblebees Artificial Life
Simulation . . . . . . . . . . . . . . . 256:1--256:1
Andreas Mayer \pkgNoisyopt: A Python library for
optimizing noisy functions . . . . . . . 258:1--258:1
Roger A. Light \pkgMosquitto: server and client
implementation of the MQTT protocol . . 265:1--265:2
Sean M. Anderson and
Bernardo S. Mendoza \pkgSHGYield . . . . . . . . . . . . . . 242:1--242:2
John P. Didion \pkgxphyle: Extraordinarily simple file
handling . . . . . . . . . . . . . . . . 255:1--255:1
Rory Nolan and
Sergi Padilla-Parra \pkgfilesstrings: An R package for file
and string manipulation . . . . . . . . 260:1--260:2
Sebastian Raschka \pkgBioPandas: Working with molecular
structures in \pkgpandas DataFrames . . 279:1--279:1
Bennett Kleinberg and
Maximilian Mozes Web-based text anonymization with
\pkgNode.js: Introducing NETANOS (Named
entity-based Text Anonymization for Open
Science) . . . . . . . . . . . . . . . . 293:1--293:2
Taylor B. Arnold \pkgkerasR: R Interface to the Keras
Deep Learning Library . . . . . . . . . 296:1--296:1
Mark Padgham and
Robin Lovelace and
Maëlle Salmon and
Bob Rudis \pkgosmdata . . . . . . . . . . . . . . 305:1--305:1
Dominik Moritz Text detection in screen images with a
Convolutional Neural Network . . . . . . 235:1--235:1
Daniel Standage and
Ali Aliyari and
Lisa J. Cohen and
Michael R. Crusoe and
Tim Head and
Luiz Irber and
Shannon E. K. Joslin and
N. B. Kingsley and
Kevin D. Murray and
Russell Neches and
Camille Scott and
Ryan Shean and
Sascha Steinbiss and
Cait Sydney and
C. Titus Brown \pkgkhmer release v2.1: software for
biological sequence analysis . . . . . . 272:1--272:2
Alexander Bock and
Emil Axelsson and
Karl Bladin and
Jonathas Costa and
Gene Payne and
Matthew Territo and
Joakim Kilby and
Masha Kuznetsova and
Carter Emmart and
Anders Ynnerman \pkgOpenSpace: An open-source
astrovisualization framework . . . . . . 281:1--281:1
Bede Constantinides and
David L. Robertson \pkgKindel: indel-aware consensus for
nucleotide sequence alignments . . . . . 282:1--282:2
Daniele De Vecchi and
Fabio Dell'Acqua and
Daniel Aurelio Galeazzo \pkgCLOOPSy --- Copernicus Land cOver
crOwdsourcing Platform for
Sentinel-based mapping . . . . . . . . . 291:1--291:2
Nima S. Hejazi and
Weixin Cai and
Alan E. Hubbard \pkgbiotmle: Targeted Learning for
Biomarker Discovery . . . . . . . . . . 295:1--295:4
Anush Krishnan and
Olivier Mesnard and
Lorena A. Barba \pkgcuIBM: a GPU-based immersed boundary
method code . . . . . . . . . . . . . . 301:1--301:1
Paul Francis Harrison \pkgVaristran: Anscombe's variance
stabilizing transformation for RNA-seq
gene expression data . . . . . . . . . . 257:1--257:1
Danny Hermes Helper for Bézier Curves, Triangles, and
Higher Order Objects . . . . . . . . . . 267:1--267:3
Pi-Yueh Chuang and
Lorena A. Barba \pkgAmgXWrapper: An interface between
\pkgPETSc and the NVIDIA \pkgAmgX
library . . . . . . . . . . . . . . . . 280:1--280:1
Lucas A. Wilson and
John M. Fonner and
Jason Allison and
Oscar Esteban and
Harry Kenya and
Marshall Lerner \pkgLauncher: A simple tool for
executing high throughput computing
workloads . . . . . . . . . . . . . . . 289:1--289:2
Edmund Noel Dawe and
Piti Ongmongkolkul and
Giordon Stark \pkgroot\_numpy: The interface between
\pkgROOT and \pkgNumPy . . . . . . . . . 307:1--307:2
Simon J. van Heeringen \pkggenomepy: download genomes the easy
way . . . . . . . . . . . . . . . . . . 320:1--320:1
Konstantin Stadler The country converter \pkgcoco --- a
Python package for converting country
names between different classification
schemes . . . . . . . . . . . . . . . . 332:1--332:2
Maëlle Salmon and
Sreekanth Vakacherla and
Carles Mil\`a and
Julian D. Marshall and
Cathryn Tonne \pkgrtimicropem: an R package supporting
the analysis of RTI MicroPEM output
files . . . . . . . . . . . . . . . . . 333:1--333:1
Mathew W. McLean \pkgRefManageR: Import and Manage BibTeX
and BibLaTeX References in R . . . . . . 338:1--338:2
P. James Joyce \pkgLcopt --- An interactive tool for
creating fully parameterised Life Cycle
Assessment (LCA) foreground models . . . 339:1--339:1
Francesco Strozzi and
Raoul Jean Pierre Bonnal \pkgPipengine: an ultra light YAML-based
pipeline execution engine . . . . . . . 341:1--341:2
Juanjo Bazán and
Oscar Gonzalez-Recio \pkgNimbus: a Ruby gem to implement
Random Forest algorithms in a genomic
selection context . . . . . . . . . . . 351:1--351:3
Thomas Cokelaer and
Dimitri Desvillechabrol and
Rachel Legendre and
Mélissa Cardon '\pkgSequana': a Set of Snakemake NGS
pipelines . . . . . . . . . . . . . . . 352:1--352:2
Sebastiano Ferraris and
Dzhoshkun Ismail Shakir and
Johannes Van Der Merwe and
Willy Gsell and
Jan Deprest and
Tom Vercauteren \pkgBruker2nifti: Magnetic Resonance
Images converter from Bruker
\pkgParaVision to \pkgNifti format . . . 354:1--354:2
Nicholas Tierney \pkgvisdat: Visualising Whole Data
Frames . . . . . . . . . . . . . . . . . 355:1--355:2
Alicia N. Schep and
Sarah K. Kummerfeld \pkgiheatmapr: Interactive complex
heatmaps in R . . . . . . . . . . . . . 359:1--359:1
Philipp S. Sommer The \pkgpsyplot interactive
visualization framework . . . . . . . . 363:1--363:1
Tanner C. Hobson and
Mathieu Doucet and
Ricardo M. Ferraz Leal \pkgDjango Remote Submission . . . . . . 366:1--366:2
Benjamin J. Morgan \pkgbsym: A basic symmetry module . . . 370:1--370:2
Sepand Haghighi \pkgPyrgg: Python Random Graph Generator 331:1--331:2
Ashlee N. Ford Versypt and
Grace K. Harrell and
Alexandra N. McPeak \pkgACEInhibPKPD: An open-source MATLAB
app for a
pharmacokinetic/pharmacodynamic model of
ACE inhibition . . . . . . . . . . . . . 340:1--340:2
Adrian M. Price-Whelan and
Daniel Foreman-Mackey \pkgschwimmbad: A uniform interface to
parallel processing pools in Python . . 357:1--357:2
Marco van Hulten \pkgComPlot: Comparison Plotter to
visually evaluate ocean model
simulations . . . . . . . . . . . . . . 368:1--368:4
Sebastien Binet and
Bastian Wieck and
David Blyth and
Emmanuel Busato and
Michaël Ughetto and
Peter Waller \pkgGo-HEP: libraries for High Energy
Physics analyses in Go . . . . . . . . . 372:1--372:4
Shane J. Latham \pkgarray\_split: Multi-dimensional
array partitioning . . . . . . . . . . . 373:1--373:2
Jakob Bossek \pkgmcMST: A Toolbox for the
Multi-Criteria Minimum Spanning Tree
Problem . . . . . . . . . . . . . . . . 374:1--374:2
Pradeep Reddy Raamana and
Stephen C. Strother \pkgPython class defining a machine
learning dataset ensuring key-based
correspondence and maintaining integrity 382:1--382:1
Benjamin W. L. Margolis \pkgSimuPy: A Python framework for
modeling and simulating dynamical
systems . . . . . . . . . . . . . . . . 396:1--396:1
Travis Kessler and
John Hunter Mack \pkgECNet: Large scale machine learning
projects for fuel property prediction 401:1--401:2
Michael Kane \pkgbittrex: An R client for the Bittrex
Crypto-Currency Exchange . . . . . . . . 402:1--402:1
Adam H. Sparks and
Mark Padgham and
Hugh Parsonage and
Keith Pembleton \pkgbomrang: Fetch Australian Government
Bureau of Meteorology Data in R . . . . 411:1--411:2
R. Daniel Kortschak and
David L. Adelson \pkgbíogo/ncbi: interfaces to NCBI
services for the Go language . . . . . . 234:1--234:2
Offray Vladimir Luna Cárdenas \pkgGrafoscopio: A moldable tool for
literate computing and reproducible
research . . . . . . . . . . . . . . . . 251:1--251:2
Thomas Cokelaer and
Juergen Hasch \pkg'Spectrum': Spectral Analysis in
Python . . . . . . . . . . . . . . . . . 348:1--348:2
Marcin Wojdyr \pkgUglyMol: a WebGL macromolecular
viewer focused on the electron density 350:1--350:2
Conrad Sanderson and
Ryan Curtin \pkggmm\_diag and \pkggmm\_full: C++
classes for multi-threaded Gaussian
mixture models and
Expectation-Maximisation . . . . . . . . 365:1--365:2
Gabriele Rovigatti Production Function Estimation in R: The
\pkgprodest Package . . . . . . . . . . 371:1--371:1
Sara Mahar and
Matthew Bellis \pkghmis: A python tool to visualize and
analyze HMIS data . . . . . . . . . . . 384:1--384:2
Adrian M. Price-Whelan \pkgGala: A Python package for galactic
dynamics . . . . . . . . . . . . . . . . 388:1--388:2
Ben Lauwens \pkgResumableFunctions: C# sharp style
generators for Julia . . . . . . . . . . 400:1--400:2
Philip Stegmaier and
Alexander Kel and
Edgar Wingender \pkggeneXplainR: An R interface for the
geneXplain platform . . . . . . . . . . 412:1--412:3
Tim Folsom and
V. P. Nagraj \pkghei: Calculate Healthy Eating Index
(HEI) Scores . . . . . . . . . . . . . . 417:1--417:1
Bérénice Batut and
Björn Grüning \pkgENASearch: A Python library for
interacting with ENA's API . . . . . . . 418:1--418:1
Andrew C. Heusser and
Paxton C. Fitzpatrick and
Campbell E. Field and
Kirsten Ziman and
Jeremy R. Manning \pkgQuail: A Python toolbox for
analyzing and plotting free recall data 424:1--424:2
Vanessa Sochat Singularity Registry: Open Source
Registry for Singularity Images . . . . 426:1--426:3
Kivan Polimis and
Ariel Rokem and
Bryna Hazelton Confidence Intervals for Random Forests
in Python . . . . . . . . . . . . . . . 124:1--124:4
Dominique Makowski and
Léo Dutriaux \pkgNeuropsydia.py: A Python Module for
Creating Experiments, Tasks and
Questionnaires . . . . . . . . . . . . . 259:1--259:2
Natalia C. Clementi and
Gilbert Forsyth and
Christopher D. Cooper and
Lorena A. Barba \pkgPyGBe-LSPR: Python and GPU
Boundary-integral solver for
electrostatics . . . . . . . . . . . . . 306:1--306:2
Pradeep Reddy Raamana and
Stephen C. Strother Histogram-weighted Networks for Feature
Extraction, Connectivity and Advanced
Analysis in Neuroscience . . . . . . . . 380:1--380:3
Yuxuan Zhang and
Jean Bilheux \pkgImagingReso: A Tool for Neutron
Resonance Imaging . . . . . . . . . . . 407:1--407:3
Andrew P. Smith \pkgUKCensusAPI: python and R interfaces
to the nomisweb UK census data API . . . 408:1--408:1
Haytham M. Fayek \pkgMatDL: A Lightweight Deep Learning
Library in MATLAB . . . . . . . . . . . 413:1--413:2
Carlos X. Hernández and
Vijay S. Pande \pkgMDEntropy: Information-Theoretic
Analyses for Molecular Dynamics . . . . 427:1--427:2
José Jiménez and
Josep Ginebra \pkgpyGPGO: Bayesian Optimization for
Python . . . . . . . . . . . . . . . . . 431:1--431:3
Marcus D. Bloice and
Christof Stocker and
Andreas Holzinger \pkgAugmentor: An Image Augmentation
Library for Machine Learning . . . . . . 432:1--432:2
Philippe Renard \pkgHytool: an open source MATLAB
toolbox for the interpretation of
hydraulic tests using analytical
solutions . . . . . . . . . . . . . . . 441:1--441:3
Henry Kironde and
Benjamin D. Morris and
Akash Goel and
Andrew Zhang and
Akshay Narasimha and
Shivam Negi and
David J. Harris and
Deborah Gertrude Digges and
Kapil Kumar and
Amritanshu Jain and
Kunal Pal and
Kevinkumar Amipara and
Prabh Simran Singh Baweja and
Ethan P. White \pkgRetriever: Data Retrieval Tool . . . 451:1--451:1
Carl Boettiger Generating \pkgCodeMeta Metadata for R
Packages . . . . . . . . . . . . . . . . 454:1--454:1
George Datseris \pkgDynamicalBilliards.jl: An
easy-to-use, modular and extendable
Julia package for Dynamical Billiard
systems in two dimensions . . . . . . . 458:1--458:4
Andre Schmeißer and
Daniel Burkhart and
Dominik Linn and
Johannes Schnebele and
Manuel Ettmüller and
Simone Gramsch and
Walter Arne \pkgEnsight4Matlab: read, process, and
write files in EnSight\reg Gold format
from C++ or MATLAB\reg . . . . . . . . . 217:1--217:1
Rohan Dandage and
Kausik Chakraborty \pkgdms2dfe: Comprehensive Workflow for
Analysis of Deep Mutational Scanning
Data . . . . . . . . . . . . . . . . . . 362:1--362:3
Ilja Honkonen High-Dimensional Integrator . . . . . . 437:1--437:1
Olivier Delestre and
Frédéric Darboux and
François James and
Carine Lucas and
Christian Laguerre and
Stéphane Cordier \pkgFullSWOF: Full Shallow-Water
equations for Overland Flow . . . . . . 448:1--448:1
Sachin Chitta and
Eitan Marder-Eppstein and
Wim Meeussen and
Vijay Pradeep and
Adolfo Rodríguez Tsouroukdissian and
Jonathan Bohren and
David Coleman and
Bence Magyar and
Gennaro Raiola and
Mathias Lüdtke and
Enrique Fernandez Perdomo \pkgros\_control: A generic and simple
control framework for ROS . . . . . . . 456:1--456:5
Ai Okada and
Kenichi Chiba and
Hiroko Tanaka and
Satoru Miyano and
Yuichi Shiraishi A framework for generating interactive
reports for cancer genome analysis . . . 457:1--457:4
Daniel Suess and
Milan Holzäpfel \pkgmpnum: A matrix product
representation library for Python . . . 465:1--465:2
Mark Padgham and
Richard Ellison \pkgbikedata . . . . . . . . . . . . . . 471:1--471:1
Steve Lockley and
Claudio Benghi and
Martin \vCerný \pkgXbim.Essentials: a library for
interoperable building information
applications . . . . . . . . . . . . . . 473:1--473:3
David J. Harris An easy-to-use \pkgp5.js $3$D object
picker for visual artists . . . . . . . 475:1--475:2
Sam Albers \pkgtidyhydat: Extract and Tidy Canadian
Hydrometric Data . . . . . . . . . . . . 511:1--511:4
Sinan Shi and
David Pérez-Suárez and
Steve Harris and
Niall MacCallum and
David Brealey and
Mervyn Singer and
James Hetherington Critical care data processing tools . . 513:1--513:4
Brandon LeBeau \pkghighlightHTML: CSS Formatting of R
Markdown Documents . . . . . . . . . . . 185:1--185:2
Gilbert Marzolin and
Olivier Gimenez Fitting a Gamma--Gompertz survival model
to capture-recapture data collected on
free-ranging animal populations . . . . 216:1--216:3
Alexander Lindsay and
Kathryn Huff \pkgMoltres: finite element based
simulation of molten salt reactors . . . 298:1--298:2
Jason K. Moore and
Antonie van den Bogert \pkgopty: Software for trajectory
optimization and parameter
identification using direct collocation 300:1--300:4
Paul B. Govan \pkgBayesianNetwork: Interactive
Bayesian Network Modeling and Analysis 425:1--425:2
Lester James V. Miranda \pkgPySwarms: a research toolkit for
Particle Swarm Optimization in Python 433:1--433:2
Jiao Y. Y. Lin and
Fahima Islam and
Max Kresh \pkgMultiphonon: Phonon Density of
States tools for Inelastic Neutron
Scattering Powder Data . . . . . . . . . 440:1--440:2
Nathan Sheffield and
V. P. Nagraj and
Vince Reuter \pkgsimpleCache: R caching for
reproducible, distributed, large-scale
projects . . . . . . . . . . . . . . . . 463:1--463:1
Markus J. Ankenbrand and
Simon Pfaff and
Niklas Terhoeven and
Musga Qureischi and
Maik Gündel and
Clemens L. Weiß and
Thomas Hackl and
Frank Förster \pkgchloroExtractor: extraction and
assembly of the chloroplast genome from
whole genome shotgun data . . . . . . . 464:1--464:3
Anton Rodenhauser and
Wilson W. Good and
Brian Zenger and
Jess Tate and
Kedar Aras and
Brett Burton and
Rob S. MacLeod \pkgPFEIFER: Preprocessing Framework for
Electrograms Intermittently Fiducialized
from Experimental Recordings . . . . . . 472:1--472:2
Pablo G. Garay and
Jorge A. Vila and
Osvaldo A. Martin \pkgCheSweet: An application to predict
glycan's chemicals shifts . . . . . . . 488:1--488:2
Björn Dahlgren \pkgpyodesys: Straightforward numerical
integration of ODE systems from Python 490:1--490:2
Pamphile T. Roy and
Sophie Ricci and
Romain Dupuis and
Robin Campet and
Jean-Christophe Jouhaud and
Cyril Fournier \pkgBATMAN: Statistical analysis for
expensive computer codes made easy . . . 493:1--493:2
René L. Warren Visualizing genome synteny with
\pkgxmatchview . . . . . . . . . . . . . 497:1--497:4
William D. McGinnis and
Chapman Siu and
Andre S. and
Hanyu Huang Category Encoders: a
\pkgscikit-learn-contrib package of
transformers for encoding categorical
data . . . . . . . . . . . . . . . . . . 501:1--501:2
Jeremy R. Coyle and
Nima S. Hejazi \pkgorigami: A Generalized Framework for
Cross-Validation in R . . . . . . . . . 512:1--512:3
Stephanie J. Spielman \pkgphyphy: Python package for
facilitating the execution and parsing
of HyPhy standard analyses . . . . . . . 514:1--514:1
R. Daniel Kortschak \pkgarrgh: a Go interface to the OpenCPU
R server system . . . . . . . . . . . . 517:1--517:1
Björn Dahlgren \pkgpyneqsys: Solve symbolically defined
systems of non-linear equations
numerically . . . . . . . . . . . . . . 531:1--531:2
Sébastien Boisgérault \pkgBitstream --- Binary Data for Humans 541:1--541:2
Joshua T. Karpel \pkgIDESolver: a general purpose
integro-differential equation solver . . 542:1--542:2
William Michael Landau The \pkgdrake R package: a pipeline
toolkit for reproducibility and
high-performance computing . . . . . . . 550:1--550:1
Benny Malengier and
Pavol Ki\vson and
James Tocknell and
Claas Abert and
Florian Bruckner and
Marc-Antonio Bisotti \pkgODES: a high level interface to ODE
and DAE solvers . . . . . . . . . . . . 165:1--165:2
James Hiebert and
Alex J. Cannon and
Trevor Murdock and
Stephen Sobie and
Arelia Werner \pkgClimDown: Climate Downscaling in R 360:1--360:1
Danilo Freire and
Robert Myles McDonnell \pkgprisonbrief: An R package that
returns tidy data from the World Prison
Brief website . . . . . . . . . . . . . 361:1--361:1
Shadia Mikhael and
Calum Gray \pkgMasks2Metrics (M2M): A Matlab
Toolbox for Gold Standard Morphometrics 436:1--436:3
Dominique Makowski The \pkgpsycho Package: an Efficient and
Publishing-Oriented Workflow for
Psychological Science . . . . . . . . . 470:1--470:2
James P. Howard II Phonetic Algorithms in R . . . . . . . . 480:1--480:2
Parker Owan and
Cameron Devine and
W. Tony Piaskowy \pkgCoreRobotics: An object-oriented C++
library with cross-language wrappers for
cross-platform robot control . . . . . . 489:1--489:2
Jeongseok Lee and
Michael X. Grey and
Sehoon Ha and
Tobias Kunz and
Sumit Jain and
Yuting Ye and
Siddhartha S. Srinivasa and
Mike Stilman and
C. Karen Liu \pkgDART: Dynamic Animation and Robotics
Toolkit . . . . . . . . . . . . . . . . 500:1--500:3
Roderick Bovee and
Nick Greenfield \pkgFinch: a tool adding dynamic
abundance filtering to genomic
MinHashing . . . . . . . . . . . . . . . 505:1--505:2
Kevin M. Moerman \pkgGIBBON: The Geometry and Image-Based
Bioengineering add-On . . . . . . . . . 506:1--506:4
Robert Gieseke and
Sven N. Willner and
Matthias Mengel \pkgPymagicc: A Python wrapper for the
simple climate model MAGICC . . . . . . 516:1--516:3
Vanessa Sochat The Experiment Factory: Reproducible
Experiment Containers . . . . . . . . . 521:1--521:4
Taha Zaghdoudi \pkgivporbit: An R package to estimate
the instrumental variables probit model 523:1--523:1
Niklas Terhoeven and
Jörg Schultz and
Thomas Hackl \pkgreper: Genome-wide identification,
classification and quantification of
repetitive elements without an assembled
genome . . . . . . . . . . . . . . . . . 527:1--527:4
Jakob Bossek \pkggrapherator: A Modular Multi-Step
Graph Generator . . . . . . . . . . . . 528:1--528:3
Nicola Demo and
Marco Tezzele and
Gianluigi Rozza \pkgPyDMD: Python Dynamic Mode
Decomposition . . . . . . . . . . . . . 530:1--530:3
Matthew Pitkin \pkgpsrqpy: a python interface for
querying the ATNF pulsar catalogue . . . 538:1--538:2
Aleksey Bilogur \pkgMissingno: a missing data
visualization suite . . . . . . . . . . 547:1--547:4
Robert Reinecke \pkgG$^3$M-f a global gradient-based
groundwater modelling framwork . . . . . 548:1--548:2
Matilda Åslin and
Monika Brandt and
Johan Dahlberg \pkgCheckQC: Quick quality control of
Illumina sequencing runs . . . . . . . . 556:1--556:2
Julia Wrobel \pkgregister: Registration for
Exponential Family Functional Data . . . 557:1--557:2
Chi-Lin Yu and
Ching-Fan Sheu \pkgEFAshiny: An User-Friendly Shiny
Application for Exploratory Factor
Analysis . . . . . . . . . . . . . . . . 567:1--567:2
Anonymous \pkgChebTools: C++11 (and Python) tools
for working with Chebyshev expansions 569:1--569:3
Stefanie E. LaZerte and
Sam Albers \pkgweathercan: Download and format
weather data from Environment and
Climate Change Canada . . . . . . . . . 571:1--571:2
James Tocknell \pkgh5preserve: Thin wrapper around
\pkgh5py, inspired by \pkgcamel . . . . 581:1--581:2
Lincoln A. Mullen and
Jordan Bratt \pkgUSAboundaries: Historical and
Contemporary Boundaries of the United
States of America . . . . . . . . . . . 314:1--314:2
Nuno Fachada and
Agostinho C. Rosa \pkgmicompm: A MATLAB/Octave toolbox for
multivariate independent comparison of
observations . . . . . . . . . . . . . . 430:1--430:1
David J. Mulryne and
John W. Ronayne \pkgPyTransport: A Python package for
the calculation of inflationary
correlation functions . . . . . . . . . 494:1--494:2
Pierre Morel \pkgGramm: grammar of graphics plotting
in Matlab . . . . . . . . . . . . . . . 568:1--568:4
Peter Laurinec \pkgTSrepr R package: Time Series
Representations . . . . . . . . . . . . 577:1--577:2
Michael Hirsch \pkgPyMap3D: $3$-D coordinate
conversions for terrestrial and geospace
environments . . . . . . . . . . . . . . 580:1--580:2
John Mount and
Nina Zumel The \pkgvtreat R package: a
statistically sound data processor for
predictive modeling . . . . . . . . . . 584:1--584:2
Donald E. Willcox and
Michael Zingale \pkgpynucastro: an interface to nuclear
reaction rates and code generator for
reaction network equations . . . . . . . 588:1--588:3
Sander Wahls and
Shrinivas Chimmalgi and
Peter J. Prins \pkgFNFT: A Software Library for
Computing Nonlinear Fourier Transforms 597:1--597:2
George Datseris \pkgDynamicalSystems.jl: A Julia
software library for chaos and nonlinear
dynamics . . . . . . . . . . . . . . . . 598:1--598:5
Andreas Bender and
Alexander Bauer \pkgcoalitions: Coalition probabilities
in multi-party democracies . . . . . . . 606:1--606:2
Grega Vrban\vci\vc and
Lucija Brezo\vcnik and
Uro\vs Mlakar and
Du\vsan Fister and
Iztok Fister, Jr. \pkgNiaPy: Python microframework for
building nature-inspired algorithms . . 613:1--613:3
Joe Thorley \pkgcheckr: An R package for Assertive
Programming . . . . . . . . . . . . . . 624:1--624:1
Konstantinos Vantas \pkghydroscoper: R interface to the
Greek National Data Bank for
Hydrological and Meteorological
Information . . . . . . . . . . . . . . 625:1--625:2
Rory Nolan and
Sergi Padilla-Parra \pkgijtiff: An R package providing TIFF
I/O for ImageJ users . . . . . . . . . . 633:1--633:2
Alessandro Gasparini \pkgcomorbidity: An R package for
computing comorbidity scores . . . . . . 648:1--648:3
Lincoln A. Mullen and
Kenneth Benoit and
Os Keyes and
Dmitry Selivanov and
Jeffrey Arnold Fast, Consistent Tokenization of Natural
Language Text . . . . . . . . . . . . . 655:1--655:3
Björn Dahlgren \pkgChemPy: A package useful for
chemistry written in Python . . . . . . 565:1--565:2
Sergio Ibarra-Espinosa and
Daniel Schuch and
Edmilson Dias de Freitas \pkgeixport: An R package to export
emissions to atmospheric models . . . . 607:1--607:4
Giuseppe Cardellini and
Chris Mutel \pkgTemporalis: an open source software
for dynamic LCA . . . . . . . . . . . . 612:1--612:2
Patrick K. Mogensen and
Asbjòrn N. Riseth \pkgOptim: A mathematical optimization
package for Julia . . . . . . . . . . . 615:1--615:3
Daniel Amsel and
André Billion and
Andreas Vilcinskas and
Frank Förster \pkgmicroPIECE --- microRNA pipeline
enhanced by CLIP experiments . . . . . . 616:1--616:4
Louise A. Dennis The MCAPL Framework including the Agent
Infrastructure Layer and Agent Java
Pathfinder . . . . . . . . . . . . . . . 617:1--617:2
Sebastian Raschka \pkgMLxtend: Providing machine learning
and data science utilities and
extensions to Python's scientific
computing stack . . . . . . . . . . . . 638:1--638:2
Mordechai (Moti) Ben-Ari \pkgLearnSAT: A SAT Solver for Education 639:1--639:2
Casey Youngflesh \pkgMCMCvis: Tools to Visualize,
Manipulate, and Summarize MCMC Output 640:1--640:3
Caley Finn \pkgOpenEPSim: An Open Exclusion Process
Simulation Tool . . . . . . . . . . . . 650:1--650:2
Michael Hucka \pkgSpiral: splitters for identifiers in
source code files . . . . . . . . . . . 653:1--653:3
Yuan Tang \pkgautoplotly: An R package for
automatic generation of interactive
visualizations for statistical results 657:1--657:2
Brian E. J. Rose \pkgCLIMLAB: a Python toolkit for
interactive, process-oriented climate
modeling . . . . . . . . . . . . . . . . 659:1--659:2
Nicola Demo and
Marco Tezzele and
Gianluigi Rozza \pkgEZyRB: Easy Reduced Basis method . . 661:1--661:3
Jasper Ginn \pkgqualtRics: retrieve survey data
using the Qualtrics API . . . . . . . . 690:1--690:1
Júlio Hoffimann \pkgGeoStats.jl --- High-performance
geostatistics in Julia . . . . . . . . . 692:1--692:4
Sebastian S. Zeki \pkgEndoMineR for the extraction of
endoscopic and associated pathology data
from medical reports . . . . . . . . . . 701:1--701:2
Benjamin Allévius \pkgscanstatistics: space-time anomaly
detection using scan statistics . . . . 515:1--515:2
Pi-Yueh Chuang and
Olivier Mesnard and
Anush Krishnan and
Lorena A. Barba \pkgPetIBM: toolbox and applications of
the immersed-boundary method on
distributed-memory architectures . . . . 558:1--558:5
Ignacio Ferrés and
Gregorio Iraola \pkgPhylen: automatic phylogenetic
reconstruction using the EggNOG database 593:1--593:3
Michael Hucka \pkgNostril: A nonsense string evaluator
written in Python . . . . . . . . . . . 596:1--596:2
Mike Innes \pkgFlux: Elegant machine learning with
Julia . . . . . . . . . . . . . . . . . 602:1--602:1
Dave Hudak and
Doug Johnson and
Alan Chalker and
Jeremy Nicklas and
Eric Franz and
Trey Dockendorf and
Brian L. McMichael Open OnDemand: A web-based client portal
for HPC centers . . . . . . . . . . . . 622:1--622:2
Andrew P. Smith \pkghumanleague: a C++ microsynthesis
package with R and Python interfaces . . 629:1--629:1
Ryan C. Brown and
Joshua Moser \pkgHSImage: A Python and C++ library to
allow interaction with ENVI-BIL
hyperspectral images . . . . . . . . . . 630:1--630:2
Amelia Ortiz-Gil and
Jordi Burguet-Castell Mapelia and friends: create $3$D models
from maps . . . . . . . . . . . . . . . 660:1--660:2
Arjun Chennu \pkgMicroBenthos: a modeling framework
for microbial benthic ecology . . . . . 674:1--674:2
Mikkel Meyer Andersen \pkgmalan: MAle Lineage ANalysis . . . . 684:1--684:2
Boaz Blankrot and
Clemens Heitzinger \pkgParticleScattering: Solving and
optimizing multiple-scattering problems
in Julia . . . . . . . . . . . . . . . . 691:1--691:3
Jacob Anhòj \pkgqicharts2: Quality Improvement
Charts for R . . . . . . . . . . . . . . 699:1--699:2
William D. Pearse and
Scott A. Chamberlain \pkgSuppdata: Downloading Supplementary
Data from Published Manuscripts . . . . 721:1--721:2
Sepand Haghighi and
Masoomeh Jasemi and
Shaahin Hessabi and
Alireza Zolanvari \pkgPyCM: Multiclass confusion matrix
library in Python . . . . . . . . . . . 729:1--729:2
Stephen D. Turner \pkgqqman: an R package for visualizing
GWAS results using Q-Q and Manhattan
plots . . . . . . . . . . . . . . . . . 731:1--731:2
Ryan G. James and
Christopher J. Ellison and
James P. Crutchfield \pkgdit: a Python package for discrete
information theory . . . . . . . . . . . 738:1--738:3
Richard Izzo and
David Steinman and
Simone Manini and
Luca Antiga The Vascular Modeling Toolkit: A Python
Library for the Analysis of Tubular
Structures in Medical Images . . . . . . 745:1--745:5
Anonymous \pkgkima: Exoplanet detection in radial
velocities . . . . . . . . . . . . . . . 487:1--487:3
Antoine Cully and
Konstantinos Chatzilygeroudis and
Federico Allocati and
Jean-Baptiste Mouret \pkgLimbo: A Flexible High-performance
Library for Gaussian Processes modeling
and Data-Efficient Optimization . . . . 545:1--545:3
Edward W. Doddridge and
Alexey Radul \pkgAronnax: An idealised isopycnal
ocean model . . . . . . . . . . . . . . 592:1--592:2
Laurent Fasnacht \pkgmmappickle: Python 3 module to store
memory-mapped \pkgnumpy array in
\pkgpickle format . . . . . . . . . . . 651:1--651:2
Tobias C. Wood \pkgQUIT: QUantitative Imaging Tools . . 656:1--656:2
Manuel Krebber and
Henrik Barthels \pkgMatchPy: Pattern Matching in Python 670:1--670:2
Gregory M. Green \pkgdustmaps: A Python interface for
maps of interstellar dust . . . . . . . 695:1--695:2
Karl Wette and
Reinhard Prix and
David Keitel and
Matthew Pitkin and
Christoph Dreissigacker and
John T. Whelan and
Paola Leaci \pkgOctApps: a library of Octave
functions for continuous
gravitational-wave data analysis . . . . 707:1--707:3
Shahriar Iravanian \pkgfib-tf: A TensorFlow-based Cardiac
Electrophysiology Simulator . . . . . . 719:1--719:2
Ryan R. Curtin and
Marcus Edel and
Mikhail Lozhnikov and
Yannis Mentekidis and
Sumedh Ghaisas and
Shangtong Zhang \pkgmlpack 3: a fast, flexible machine
learning library . . . . . . . . . . . . 726:1--726:2
Inom Mirzaev and
Drew F. K. Williamson and
Jacob G. Scott \pkgegtplot: A Python Package for
Three-Strategy Evolutionary Games . . . 735:1--735:4
Alessandro Gasparini \pkgrsimsum: Summarise results from
Monte Carlo simulation studies . . . . . 739:1--739:3
James Bourbeau and
Zigfried Hampel-Arias \pkgPyUnfold: A Python package for
iterative unfolding . . . . . . . . . . 741:1--741:3
Mikkel Meyer Andersen Discrete Laplace mixture model with
applications in forensic genetics . . . 748:1--748:3
Daniel G. A. Smith and
Johnnie Gray \pkgopt\_einsum --- A Python package for
optimizing contraction order for
einsum-like expressions . . . . . . . . 753:1--753:3
Daniel Lüdecke \pkgsjmisc: Data and Variable
Transformation Functions . . . . . . . . 754:1--754:2
Hajk-Georg Drost \pkgPhilentropy: Information Theory and
Distance Quantification with R . . . . . 765:1--765:4
Jeroen F. J. Laros General binary file parser . . . . . . . 766:1--766:1
Daniel Lüdecke \pkgggeffects: Tidy Data Frames of
Marginal Effects from Regression Models 772:1--772:5
Adam J. Jackson and
Alex M. Ganose and
Anna Regoutz and
Russell G. Egdell and
David O. Scanlon \pkgGalore: Broadening and weighting for
simulation of photoelectron spectroscopy 773:1--773:6
Vanessa Sochat \pkgHelpMe Command Line Helper Utility 775:1--775:3
David H. Hagan and
Andrew Tolmie and
Jakub Trochim \pkgpy-opc: operate the Alphasense
OPC-N2 from a raspberry pi or other
popular microcontrollers/microcomputers 782:1--782:2
Christoph Molnar and
Giuseppe Casalicchio and
Bernd Bischl \pkgiml: An R package for Interpretable
Machine Learning . . . . . . . . . . . . 786:1--786:2
Shaun P. Wilkinson and
Simon K. Davy \pkgphylogram: an R package for
phylogenetic analysis with nested lists 790:1--790:2
Brandon LeBeau \pkgpdfsearch: Search Tools for PDF
Files . . . . . . . . . . . . . . . . . 668:1--668:2
Sepand Haghighi and
Kasra Askari and
Sarmin Hamidi and
Mohammad Mahdi Rahimi \pkgOPEM: Open Source PEM Cell
Simulation Tool . . . . . . . . . . . . 676:1--676:4
Russell Y. Neches and
Camille Scott \pkgSuchTree: Fast, thread-safe
computations with phylogenetic trees . . 678:1--678:3
Bryan Brancotte and
Christophe Blanchet and
Hervé Ménager A reusable tree-based web-visualization
to browse EDAM ontology, and contribute
to it . . . . . . . . . . . . . . . . . 698:1--698:4
Ashlee N. Ford Versypt and
James D. Crall and
Biswadip Dey \pkgBeeNestABM: An open-source
agent-based model of spatiotemporal
distribution of bumblebees in nests . . 718:1--718:2
Hilary J. Oliver and
Matthew Shin and
Oliver Sanders \pkgCylc: A Workflow Engine for Cycling
Systems . . . . . . . . . . . . . . . . 737:1--737:2
Amirsina Torfi \pkgSpeechPy --- A Library for Speech
Processing and Recognition . . . . . . . 749:1--749:5
Ruud van der Ham \pkgsalabim: discrete event simulation
and animation in Python . . . . . . . . 767:1--767:2
Vyas Ramasubramani and
Sharon C. Glotzer \pkgrowan: A Python package for working
with quaternions . . . . . . . . . . . . 787:1--787:3
Robert W. Schlegel and
Albertus J. Smit \pkgheatwaveR: A central algorithm for
the detection of heatwaves and
cold-spells . . . . . . . . . . . . . . 821:1--821:2
Evan Odell \pkgnomisr: Access Nomis UK Labour
Market Data . . . . . . . . . . . . . . 859:1--859:2
Jarvist Moore Frost \pkgPolaronMobility.jl: Implementation
of the Feynman variational polaron model 566:1--566:2
Kirill Tsyganov and
Andrew James Perry and
Stuart Kenneth Archer and
David Powell \pkgRNAsik: A Pipeline for complete and
reproducible RNA-seq analysis that runs
anywhere with speed and ease . . . . . . 583:1--583:3
Momar G-O Hughes \pkgMCycle: A Python package for $1$D
sizing and analysis of thermodynamic
power cycles . . . . . . . . . . . . . . 710:1--710:2
Federico Reghenzani and
Giuseppe Massari and
William Fornaciari \pkgchronovise: Measurement-Based
Probabilistic Timing Analysis framework 711:1--711:3
Alex M. Ganose and
Adam J. Jackson and
David O. Scanlon \pkgsumo: Command-line tools for
plotting and analysis of periodic ab
initio calculations . . . . . . . . . . 717:1--717:3
David Topping and
Paul Connolly and
Jonathan Reid \pkgPyBox: An automated box-model
generator for atmospheric chemistry and
aerosol simulations . . . . . . . . . . 755:1--755:2
Lucy D. Whalley \pkgeffmass: An effective mass package 797:1--797:2
Andrew P. Smith and
Tom Russell \pkgukpopulation: unified national and
subnational population estimates and
projections, including variants . . . . 803:1--803:2
Nathan J. Goldbaum and
John A. ZuHone and
Matthew J. Turk and
Kacper Kowalik and
Anna L. Rosen \pkgunyt: Handle, manipulate, and
convert data with units in Python . . . 809:1--809:11
Jean-Philippe Coene \pkgsigmajs: An R \pkghtmlwidget
interface to the \pkgsigma.js
visualization library . . . . . . . . . 814:1--814:2
Jason K. Moore and
Mont Hubbard \pkgskijumpdesign: A Ski Jump Design
Tool for Specified Equivalent Fall
Height . . . . . . . . . . . . . . . . . 818:1--818:3
Marcus D. Sherman and
Ryan E. Mills \pkgBAMnostic: an OS-agnostic toolkit
for genomic sequence analysis . . . . . 826:1--826:2
Shawn David Taylor \pkgpyPhenology: A python framework for
plant phenology modelling . . . . . . . 827:1--827:2
Philip D. Waggoner The \pkghhi Package: Streamlined
Calculation and Visualization of
Herfindahl--Hirschman Index Scores . . . 828:1--828:5
Christopher Ostrouchov and
Yanwen Zhang and
William J. Weber \pkgpysrim: Automation, Analysis, and
Plotting of SRIM Calculations . . . . . 829:1--829:3
David Wiley \pkgRISE: An R package for RISE analysis 846:1--846:1
Vincent Arel-Bundock and
Nils Enevoldsen and
C. J. Yetman \pkgcountrycode: An R package to convert
country names and country codes . . . . 848:1--848:2
Will Handley \pkgfgivenx: A Python package for
functional posterior plotting . . . . . 849:1--849:4
Steven G. Murray \pkgpowerbox: A Python package for
creating structured fields with
isotropic power spectra . . . . . . . . 850:1--850:2
Brett M. Morris and
Trevor Dorn-Wallenstein \pkgaesop: ARC Echelle Spectroscopic
Observation Pipeline . . . . . . . . . . 854:1--854:1
Raoul R. Wadhwa and
Drew F. K. Williamson and
Andrew Dhawan and
Jacob G. Scott \pkgTDAstats: R pipeline for computing
persistent homology in topological data
analysis . . . . . . . . . . . . . . . . 860:1--860:3
Michael T. Porter \pkgjs-emass: A flexible JavaScript
implementation of the \pkgemass
algorithm . . . . . . . . . . . . . . . 869:1--869:1
Andrew T. Jones and
Hien D. Nguyen and
Geoffrey J. McLachlan \pkglogKDE: log-transformed kernel
density estimation . . . . . . . . . . . 870:1--870:3
Pierre de Buyl \pkgtidynamics: A tiny package to
compute the dynamics of stochastic and
molecular simulations . . . . . . . . . 877:1--877:4
Vanessa Sochat \pkgContainershare: Open Source Registry
to build, test, deploy with CircleCI . . 878:1--878:3
Thomas Klebel \pkgjstor: Import and Analyse Data from
Scientific Texts . . . . . . . . . . . . 883:1--883:2
Jared M. Andrews and
Mohamed El-Alawi and
Jacqueline E. Payton \pkgGenotify: Fast, lightweight gene
lookup and summarization . . . . . . . . 885:1--885:4
Benjamin Williams Combining a Probability and a
Non-Probability Sample in a
Capture--Recapture Setting . . . . . . . 886:1--886:2
Anwar O. Nunez-Elizalde and
James S. Gao and
Tianjiao Zhang and
Jack L. Gallant \pkgcottoncandy: scientific python
package for easy cloud storage . . . . . 890:1--890:2
David N. Sousa and
João R. Daniel \pkgbor: An R Package for Transforming
Behavioral Observation Records into Data
Matrices . . . . . . . . . . . . . . . . 909:1--909:4
Simon Dirmeier \pkgdatastructures: An R package for
organisation and storage of data . . . . 910:1--910:2
Lionel Roubeyrie and
Sébastien Celles \pkgWindrose: A Python \pkgMatplotlib,
\pkgNumpy library to manage wind and
pollution data, draw windrose . . . . . 268:1--268:5
David P. Fleming and
Jake VanderPlas \pkgapproxposterior: Approximate
Posterior Distributions in Python . . . 781:1--781:2
Johnnie Gray \pkgquimb: A python package for quantum
information and many-body calculations 819:1--819:3
Stefan Pfenninger and
Bryn Pickering \pkgCalliope: a multi-scale energy
systems modelling framework . . . . . . 825:1--825:2
Leland McInnes and
John Healy and
Nathaniel Saul and
Lukas Großberger \pkgUMAP: Uniform Manifold Approximation
and Projection . . . . . . . . . . . . . 861:1--861:2
Palash Goyal and
Emilio Ferrara \pkgGEM: A Python package for graph
embedding methods . . . . . . . . . . . 876:1--876:2
William F. Holmgren and
Clifford W. Hansen and
Mark A. Mikofski \pkgpvlib python: a python package for
modeling solar energy systems . . . . . 884:1--884:3