Journal of open source software

Keyphrases

Publications

volume 7, number 70, 2022

Alexander P Rockhill, Eric Larson, Brittany Stedelin, Alessandra Mantovani, Ahmed M Raslan, Alexandre Gramfort, Nicole C Swann
Intracranial Electrode Location and Analysis in MNE-Python. Journal of open source software 7 (70) (2022)

volume 7, number 71, 2022

Benjamin M Gyori, Charles Tapley Hoyt
PyBioPAX: biological pathway exchange in Python. Journal of open source software 7 (71) (2022)
Arkajyoti Saha, Sumanta Basu, Abhirup Datta
RandomForestsGLS: An R package for Random Forests for dependent data. Journal of open source software 7 (71) (2022)
Coleman Harris, Julia Wrobel, Simon Vandekar
mxnorm: An R Package to Normalize Multiplexed Imaging Data. Journal of open source software 7 (71) (2022)
Floris Van Breugel, Yuying Liu, Bingni W Brunton, J Nathan Kutz
PyNumDiff: A Python package for numerical differentiation of noisy time-series data. Journal of open source software 7 (71) (2022)

volume 7, number 78, 2022

Ming Hu, Xiaolong Jiang
PatchView: A Python Package for Patch-clamp Data Analysis and Visualization. Journal of open source software 7 (78) (2022)

volume 7, number 79, 2022

Abraham Stroschein, Ian Delgadillo Bonequi, Lucas J Koerner
Pyripherals: A Python Package for Communicating with Peripheral Electronic Devices. Journal of open source software 7 (79) (2022)

volume 7, number 80, 2022

Christopher Pockrandt, Aleksey V Zimin, Steven L Salzberg
Metagenomic classification with KrakenUniq on low-memory computers. Journal of open source software 7 (80) (2022)

volume 6, number 57, 2021

John Huddleston, James Hadfield, Thomas R Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin, Elias Harkins, Trevor Bedford, Richard A Neher, Emma B Hodcroft
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of open source software 6 (57) (2021)

volume 6, number 58, 2021

Adam Richie-Halford, Manjari Narayan, Noah Simon, Jason Yeatman, Ariel Rokem
Groupyr: Sparse Group Lasso in Python. Journal of open source software 6 (58) (2021)

volume 6, number 59, 2021

Zeyuan Song, Anastasia Gurinovich, Anthony Federico, Stefano Monti, Paola Sebastiani
nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline. Journal of open source software 6 (59) (2021)

volume 6, number 61, 2021

Malte Brunn, Naveen Himthani, George Biros, Miriam Mehl, Andreas Mang
CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures. Journal of open source software 6 (61) (2021)
Begüm D Topçuoğlu, Zena Lapp, Kelly L Sovacool, Evan Snitkin, Jenna Wiens, Patrick D Schloss
mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. Journal of open source software 6 (61) (2021)

volume 6, number 63, 2021

Thomas P Urbach, Andrey S Portnoy
fitgrid: A Python package for multi-channel event-related time series regression modeling. Journal of open source software 6 (63) (2021)

volume 6, number 64, 2021

Cameron T Roots, Alexandra Lukasiewicz, Jeffrey E Barrick
OSTIR: open source translation initiation rate prediction. Journal of open source software 6 (64) (2021)

volume 6, number 66, 2021

Alexis M Hill, James R Rybarski, Kuang Hu, Ilya J Finkelstein, Claus O Wilke
Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets. Journal of open source software 6 (66) (2021)

volume 6, number 68, 2021

Klevis Aliaj, Heath B Henninger
Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion. Journal of open source software 6 (68) (2021)

volume 5, number 45, 2020

Albert Steppi, Benjamin M Gyori, John A Bachman
Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. Journal of open source software 5 (45) (2020)

volume 5, number 46, 2020

Josh Day, Hua Zhou
OnlineStats.jl: A Julia package for statistics on data streams. Journal of open source software 5 (46) (2020)

volume 5, number 47, 2020

Malcolm Barrett, Joshua Millstein
partition: A fast and flexible framework for data reduction in R. Journal of open source software 5 (47) (2020)
Alan F Rubin
fqfa: A pure Python package for genomic sequence files. Journal of open source software 5 (47) (2020)

volume 5, number 48, 2020

J Sebastian Paez, Michael K Wendt, Nadia Atallah Lanman
scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data. Journal of open source software 5 (48) (2020)

volume 5, number 49, 2020

Jason Cory Brunson
ggalluvial: Layered Grammar for Alluvial Plots. Journal of open source software 5 (49) (2020)
Jason Cory Brunson
ggalluvial: Layered Grammar for Alluvial Plots. Journal of open source software 5 (49) (2020)

volume 5, number 51, 2020

Kai-Cheng Yang, Brian Aronson, Yong-Yeol Ahn
BiRank: Fast and Flexible Ranking on Bipartite Networks with R and Python. Journal of open source software 5 (51) (2020)

volume 5, number 52, 2020

Sarah K Hilton, John Huddleston, Allison Black, Khrystyna North, Adam S Dingens, Trevor Bedford, Jesse D Bloom
dms-view: Interactive visualization tool for deep mutational scanning data. Journal of open source software 5 (52) (2020)

volume 5, number 53, 2020

Mitchell John Sullivan, Harm van Bakel
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes. Journal of open source software 5 (53) (2020)
Joseph D Baugher
SeroTools: a Python package for Salmonella serotype data analysis. Journal of open source software 5 (53) (2020)

volume 5, number 54, 2020

John Hoffer, Rumana Rashid, Jeremy L Muhlich, Yu-An Chen, Douglas Peter William Russell, Juha Ruokonen, Robert Krueger, Hanspeter Pfister, Sandro Santagata, Peter K Sorger
Minerva: a light-weight, narrative image browser for multiplexed tissue images. Journal of open source software 5 (54) (2020)
Roni Choudhury, Jon Beezley, Brandon Davis, Jared Tomeck, Samuel Gratzl, Lilian Golzarri-Arroyo, Jun Wan, Daniel Raftery, Jeff Baumes, Thomas M O'Connell
Viime: Visualization and Integration of Metabolomics Experiments. Journal of open source software 5 (54) (2020)
Christopher Khan, Brett Byram
GENRE (GPU Elastic-Net REgression): A CUDA-Accelerated Package for Massively Parallel Linear Regression with Elastic-Net Regularization. Journal of open source software 5 (54) (2020)
Alexander P Rockhill, Ahmed M Raslan, Nicole C Swann
pd-parser: A tool for Matching Photodiode Deflection Events to Time-Stamped Events. Journal of open source software 5 (54) (2020)

volume 5, number 56, 2020

David R Tyrpak, Yaocun Li, Siqi Lei, J Andrew MacKay
SIAL: A simple image analysis library for wet-lab scientists. Journal of open source software 5 (56) (2020)

volume 4, number 38, 2019

Frederick Boehm, Brian Yandell, Karl W Broman
qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations. Journal of open source software 4 (38) (2019)

volume 4, number 39, 2019

Adam G Diehl, Alan P Boyle
CGIMP: Real-time exploration and covariate projection for self-organizing map datasets. Journal of open source software 4 (39) (2019)
George G Vega Yon, Paul Marjoram
fmcmc: A friendly MCMC framework. Journal of open source software 4 (39) (2019)
Randy Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, Paul Macklin
xml2jupyter: Mapping parameters between XML and Jupyter widgets. Journal of open source software 4 (39) (2019)

volume 4, number 40, 2019

Tal Yarkoni, Christopher J Markiewicz, Alejandro de la Vega, Krzysztof J Gorgolewski, Taylor Salo, Yaroslav O Halchenko, Quinten McNamara, Krista DeStasio, Jean-Baptiste Poline, Dmitry Petrov, Valérie Hayot-Sasson, Dylan M Nielson, Johan Carlin, Gregory Kiar, Kirstie Whitaker, Elizabeth DuPre, Adina Wagner, Lee S Tirrell, Mainak Jas, Michael Hanke, Russell A Poldrack, Oscar Esteban, Stefan Appelhoff, Chris Holdgraf, Isla Staden, Bertrand Thirion, Dave F Kleinschmidt, John A Lee, Matteo Visconti di Oleggio Castello, Michael P Notter, Ross Blair
PyBIDS: Python tools for BIDS datasets. Journal of open source software 4 (40) (2019)
Christopher W John, Denis A Proshlyakov
KinESim: Pre-equilibrium kinetic simulation of electrochemical reactions. Journal of open source software 4 (40) (2019)
Allison M Stettler, Christopher W John, Yegor D Proshlyakov, Denis A Proshlyakov
G3F: Global, Multidimensional Spectral Regression Analysis. Journal of open source software 4 (40) (2019)

volume 4, number 42, 2019

George G Vega Yon, Paul Marjoram
slurmR: A lightweight wrapper for HPC with Slurm. Journal of open source software 4 (42) (2019)
Jorge Paolo Casas, Chandramouli Chandrasekaran
openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications. Journal of open source software 4 (42) (2019)

volume 4, number 44, 2019

Amit Min, Erika Deoudes, Marielle L Bond, Eric S Davis, Douglas H Phanstiel
CoralP: Flexible visualization of the human phosphatome. Journal of open source software 4 (44) (2019)
Mayura N Patwardhan, Craig D Wenger, Eric S Davis, Douglas H Phanstiel
Bedtoolsr: An R package for genomic data analysis and manipulation. Journal of open source software 4 (44) (2019)
Stefan Appelhoff, Matthew Sanderson, Teon L Brooks, Marijn van Vliet, Romain Quentin, Chris Holdgraf, Maximilien Chaumon, Ezequiel Mikulan, Kambiz Tavabi, Richard Höchenberger, Dominik Welke, Clemens Brunner, Alexander P Rockhill, Eric Larson, Alexandre Gramfort, Mainak Jas
MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of open source software 4 (44) (2019)
Katharine H D Crawford, Jesse D Bloom
alignparse: A Python package for parsing complex features from high-throughput long-read sequencing. Journal of open source software 4 (44) (2019)

Journal of open source software

Keyphrases

Publications

volume 8, number 82, 2023

volume 8, number 83, 2023

volume 8, number 88, 2023

volume 7, number 69, 2022

volume 7, number 70, 2022

volume 7, number 71, 2022

volume 7, number 78, 2022

volume 7, number 79, 2022

volume 7, number 80, 2022

volume 6, number 57, 2021

volume 6, number 58, 2021

volume 6, number 59, 2021

volume 6, number 61, 2021

volume 6, number 63, 2021

volume 6, number 64, 2021

volume 6, number 66, 2021

volume 6, number 68, 2021

volume 5, number 45, 2020

volume 5, number 46, 2020

volume 5, number 47, 2020

volume 5, number 48, 2020

volume 5, number 49, 2020

volume 5, number 51, 2020

volume 5, number 52, 2020

volume 5, number 53, 2020

volume 5, number 54, 2020

volume 5, number 56, 2020

volume 4, number 38, 2019

volume 4, number 39, 2019

volume 4, number 40, 2019

volume 4, number 42, 2019

volume 4, number 44, 2019