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Featured Article
https://doi.org/10.12688/f1000research.27395.2
Software Tool Article metrics
Revised
GeNePy3D: a quantitative geometry python toolbox for bioimaging
[version 2; peer review: 2 approved]
Minh-Son Phan, Anatole Chessel
Peer Reviewers Virginie Uhlmann; Yizhi Wang
  • Funder
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 17 Jun 2021
https://doi.org/10.12688/f1000research.127142.3
Software Tool Article metrics
Revised
Med-ImageTools: An open-source Python package for robust data processing pipelines and curating medical imaging data
[version 3; peer review: 2 approved]
Sejin Kim, Michal Kazmierski, Kevin Qu, Jacob Peoples, Minoru Nakano, Vishwesh Ramanathan, Joseph Marsilla, Mattea Welch, Amber Simpson, Benjamin Haibe-Kains
Peer Reviewers Rachel Sparks; Johann Faouzi
  • Funders
  • Canadian Cancer Society
  • Canadian Institutes of Health Research
LATEST VERSION PUBLISHED 07 Feb 2025
https://doi.org/10.12688/f1000research.149391.2
Software Tool Article metrics
Revised
Leveraging Quadratic Polynomials in Python for Advanced Data Analysis
[version 2; peer review: 2 approved]
Rostyslav Sipakov, Olena Voloshkina, Anastasiia Kovalova
Peer Reviewers Selim Molla; Qiao Wang
  • Funder
  • CoastalQuant, Inc. (Tampa, FL, U.S.)
LATEST VERSION PUBLISHED 20 Aug 2024
https://doi.org/10.12688/f1000research.138059.1
Method Article metrics
A tutorial hub for realising the potential of tools within the SPARC ecosystem
[version 1; peer review: 2 approved with reservations]
Niloofar Shahidi, Omkar Athavale, Yuda Munarko, Mathias Roesler, Kenneth Tran
Peer Reviewers Bhavesh Patel; Andrey Andreev
PUBLISHED 08 Jan 2024
https://doi.org/10.12688/f1000research.138349.1
Software Tool Article metrics
MotionRender: A simple Python implementation of video motion visualization for 3D motion capture data
[version 1; peer review: 1 approved]
Derek Harter, Shulan Lu
Peer Reviewers Eshin Jolly
  • Funder
  • Army Research Laboratory
PUBLISHED 08 Jan 2024
https://doi.org/10.12688/f1000research.126484.2
Software Tool Article metrics
Revised
Inglämnlagare: a tool for restructuring Swedish HER record site data for statistical analysis
[version 2; peer review: 3 approved]
Daniel Löwenborg, Filipp Antomonov
Peer Reviewers Daniella Vos; Francesco Carrer; Joe Roe
  • Funder
  • Riksbankens Jubileumsfond
LATEST VERSION PUBLISHED 17 Oct 2023
https://doi.org/10.12688/f1000research.129826.1
Software Tool Article metrics
PyRadGUI: A GUI based radiomics extractor software
[version 1; peer review: 3 approved with reservations]
Umesh B. Sherkhane, Ashish Kumar Jha, Sneha Mithun, Vinay Jaiswar, Alberto Traverso, Leonard Wee, Venkatesh Rangarajan, Andre Dekker
Peer Reviewers Nguyen Quoc Khanh Le; Seyyed Ali Hosseini; Khashayar Namdar
  • Funder
  • The Netherlands Enterprise Agency (RVO) and MeITy
PUBLISHED 10 Mar 2023
https://doi.org/10.12688/f1000research.127953.1
Software Tool Article metrics
ROOSTER: An image labeler and classifier through interactive recurrent annotation
[version 1; peer review: 1 approved with reservations]
Zhou Tang, Yang Hu, Zhiwu Zhang
Peer Reviewers Michael Schirrmann
  • Funders
  • Washington Grain Commission
  • United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA)
PUBLISHED 06 Feb 2023
https://doi.org/10.12688/f1000research.19426.2
Software Tool Article metrics
Revised
Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads
[version 2; peer review: 2 approved]
Andrian Yang, Joshua Y. S. Tang, Michael Troup, Joshua W. K. Ho
Peer Reviewers Quan Nguyen; Marco Previtali and Luca Denti
  • Funders
  • National Heart Foundation of Australia
  • Amazon Web Services
  • National Health and Medical Research Council
  • Department of Education, Australian Governement
LATEST VERSION PUBLISHED 13 Oct 2022
https://doi.org/10.12688/f1000research.123616.1
Method Article metrics
An optimized approach for class imbalance problem in heterogeneous cross project defect prediction
[version 1; peer review: 1 approved with reservations]
Lipika Goel, Neha Nandal, Sonam Gupta
Peer Reviewers Santosh Rathore
PUBLISHED 16 Sep 2022
https://doi.org/10.12688/f1000research.122840.1
Software Tool Article metrics
vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework
[version 1; peer review: 1 approved, 2 approved with reservations]
V.P. Nagraj, Matthew Scholz, Shakeel Jessa, Jianye Ge, August E. Woerner, Meng Huang, Bruce Budowle, Stephen D. Turner
Peer Reviewers Ardalan Naseri; Gianluca Della Vedova; Cristiane Taniguti
  • Funders
  • Center for Human Identification, University of North Texas Health Science Center
  • National Institute of Justice, Office of Justice Programs, U.S. Department of Justice
PUBLISHED 11 Jul 2022
https://doi.org/10.12688/f1000research.53842.2
Opinion Article metrics
Revised
Python for gene expression
[version 2; peer review: 2 approved]
Leonid Bystrykh
Peer Reviewers Sergio Peignier; Yasha Hasija
LATEST VERSION PUBLISHED 23 Jun 2022
https://doi.org/10.12688/f1000research.110194.1
Software Tool Article metrics
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
[version 1; peer review: 1 approved, 3 approved with reservations]
Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C. Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F Paulin, Muhammad Sohail Raza, Susanne P. Pfeifer, Daniel Paiva Agustinho, Elbay Aliyev, Pavel Avdeyev, Enrico R. Barrozo, Sairam Behera, Kimberley Billingsley, Li Chuin Chong, Deepak Choubey, Wouter De Coster, Yilei Fu, Alejandro R. Gener, Timothy Hefferon, David Morgan Henke, Wolfram Höps, Anastasia Illarionova, Michael D. Jochum, Maria Jose, Rupesh K. Kesharwani, Sree Rohit Raj Kolora, Jędrzej Kubica, Priya Lakra, Damaris Lattimer, Chia-Sin Liew, Bai-Wei Lo, Chunhsuan Lo, Anneri Lötter, Sina Majidian, Suresh Kumar Mendem, Rajarshi Mondal, Hiroko Ohmiya, Nasrin Parvin, Carolina Peralta, Chi-Lam Poon, Ramanandan Prabhakaran, Marie Saitou, Aditi Sammi, Philippe Sanio, Nicolae Sapoval, Najeeb Syed, Todd Treangen, Gaojianyong Wang, Tiancheng Xu, Jianzhi Yang, Shangzhe Zhang, Weiyu Zhou, Fritz J Sedlazeck, Ben Busby
Peer Reviewers Rodolfo Aramayo; Nguyen Quoc Khanh Le; Pedro G. Ferreira; Quan Long
  • Funders
  • National Library of Medicine
  • Swiss National Science Foundation
  • USDA Agricultural Research Service HQ Research Associate program in Big Data
  • Centers for Disease Control and Prevention through the Association of Public Health Laboratories
  • ALS Association Milton Safenowitz Research
  • The Research Council of Norway
  • Large Facilities Office
  • China Scholarship Council PhD scholarship
  • NIHR Maudsley Biomedical Research Centre
  • The Motor Neurone Disease Association
  • FWO
PUBLISHED 16 May 2022
https://doi.org/10.12688/f1000research.110711.1
Research Article metrics
Risk prediction model for 24-hour mortality in preterm infants using lactate and blood gas analysis: A machine learning approach and retrospective cohort study
[version 1; peer review: 2 not approved]
Felipe Yu Matsushita, Vera Lúcia Jornada Krebs, Werther Brunow de Carvalho
Peer Reviewers Thomas Wood; Fu-Sheng Chou
PUBLISHED 20 Apr 2022
https://doi.org/10.12688/f1000research.75243.1
Software Tool Article metrics
SASCRiP: A Python workflow for preprocessing UMI count-based scRNA-seq data
[version 1; peer review: 2 approved with reservations]
Darisia Moonsamy, Nikki Gentle
Peer Reviewers Fabiola Curion and Luke Zappia; Fangming Xie
  • Funder
  • National Research Foundation
PUBLISHED 15 Feb 2022
https://doi.org/10.12688/f1000research.52317.1
Software Tool Article metrics AWAITING PEER REVIEW
PressPurt: network sensitivity to press perturbations under interaction uncertainty
[version 1; peer review: awaiting peer review]
David Koslicki, Dana Gibbon, Mark Novak
Peer Reviewers Invited
  • Funder
  • National Science Foundation
PUBLISHED 11 Feb 2022
https://doi.org/10.12688/f1000research.54788.2
Software Tool Article metrics
Revised
TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data
[version 2; peer review: 2 approved]
Francesco Reina, John M.A. Wigg, Mariia Dmitrieva, Bela Vogler, Joël Lefebvre, Jens Rittscher, Christian Eggeling
Peer Reviewers Xavier Michalet; Eva Christensen Arnspang
  • Funders
  • MRC/BBSRC/EPSRC
  • Wolfson Foundation
  • Deutsche Forschungsgemeinschaft
  • John Fell Fund, University of Oxford
  • Medical Research Council
  • Fonds de recherche du Québec – Nature et technologies
  • Wellcome Collaborative Award
  • Wellcome Trust
LATEST VERSION PUBLISHED 31 Jan 2022
https://doi.org/10.12688/f1000research.79530.1
Software Tool Article metrics
bit: a multipurpose collection of bioinformatics tools
[version 1; peer review: 2 not approved]
Michael Lee
Peer Reviewers Kai Zhang; Georges Hattab
PUBLISHED 31 Jan 2022
https://doi.org/10.12688/f1000research.73492.1
Software Tool Article metrics
KnowMore: an automated knowledge discovery tool for the FAIR SPARC datasets
[version 1; peer review: 2 approved with reservations]
Ryan Quey, Matthew A. Schiefer, Anmol Kiran, Bhavesh Patel
Peer Reviewers Thomas Donoghue; Ammar Ammar
PUBLISHED 09 Nov 2021
https://doi.org/10.12688/f1000research.53287.1
Software Tool Article metrics
SureTypeSCR: R package for rapid quality control and genotyping of SNP arrays from single cells
[version 1; peer review: 1 approved, 2 approved with reservations]
Ivan Vogel, Lishan Cai, Lea Jerman-Plesec, Eva R. Hoffmann
Peer Reviewers Joris Robert Vermeesch; Jason Torres; Kun Lu Lu
  • Funders
  • Danmarks Grundforskningsfond
  • European Research Council
  • Novo Nordisk Fonden
PUBLISHED 21 Sep 2021
1-20 of 47 ARTICLES
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