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https://doi.org/10.12688/f1000research.52141.1
Software Tool Article metrics AWAITING PEER REVIEW
Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design
[version 1; peer review: awaiting peer review]
Kristianne Arielle Gabriel, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, Marc Jermaine Pontiveros, Hannah Mae Magno, Joshua Gregor Dizon, El King Morado, Jan Michael Yap
Peer Reviewers Invited
  • Funder
  • Philippine Council for Industry, Energy and Emerging Technology Research and Development of the Department of Science and Technology
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.26786.1
Software Tool Article metrics PEER REVIEW DISCONTINUED
VTES: a stochastic Python-based tool to simulate viral transmission
[version 1; peer review: awaiting peer review]
Danielle L. Kurtin, Daniel A.J. Parsons, Scott M. Stagg
Peer Reviewers Invited
  • Funders
  • University of Surrey
  • National Institutes of Health
PUBLISHED 05 Oct 2020
https://doi.org/10.12688/f1000research.15824.3
Software Tool Article metrics
Revised
sPop: Age-structured discrete-time population dynamics model in C, Python, and R
[version 3; peer review: 2 approved]
Kamil Erguler
Peer Reviewers Juliane Liepe; Matthew Silk
LATEST VERSION PUBLISHED 28 Sep 2020
https://doi.org/10.12688/f1000research.24006.1
Software Tool Article metrics
flimview : A software framework to handle, visualize and analyze FLIM data
[version 1; peer review: 1 approved, 1 approved with reservations]
Matias Carrasco Kind, Mantas Zurauskas, Aneesh Alex, Marina Marjanovic, Prabuddha Mukherjee, Minh Doan, Darold R. Spillman Jr., Steve Hood, Stephen A. Boppart
Peer Reviewers Xavier Michalet; Nirmal Mazumder
  • Funder
  • GlaxoSmithKline
PUBLISHED 08 Jun 2020
https://doi.org/10.12688/f1000research.22090.2
Research Article metrics
Revised
Machine learning meets pKa
[version 2; peer review: 2 approved]
Marcel Baltruschat, Paul Czodrowski
Peer Reviewers Ruth Brenk; Johannes Kirchmair
LATEST VERSION PUBLISHED 27 Apr 2020
https://doi.org/10.12688/f1000research.22758.1
Software Tool Article metrics
GoodVibes: automated thermochemistry for heterogeneous computational chemistry data
[version 1; peer review: 2 approved with reservations]
Guilian Luchini, Juan V. Alegre-Requena, Ignacio Funes-Ardoiz, Robert S. Paton
Peer Reviewers Robert Pollice; Kjell Jorner
  • Funder
  • National Science Foundation
PUBLISHED 24 Apr 2020
https://doi.org/10.12688/f1000research.22292.2
Software Tool Article metrics
Revised
ccbmlib – a Python package for modeling Tanimoto similarity value distributions
[version 2; peer review: 2 approved]
Martin Vogt, Jürgen Bajorath
Peer Reviewers Brian Goldman; David A. Cosgrove
LATEST VERSION PUBLISHED 05 Mar 2020
https://doi.org/10.12688/f1000research.21556.2
Software Tool Article metrics
Revised
SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence
[version 2; peer review: 1 approved, 1 approved with reservations, 1 not approved]
Peter T. Habib, Alsamman M. Alsamman, Sameh E. Hassanein, Ghada A. Shereif, Aladdin Hamwieh
Peer Reviewers Fakher Rahim; Ka-Chun Wong; Tim Kacprowski
LATEST VERSION PUBLISHED 20 Feb 2020
https://doi.org/10.12688/f1000research.19541.3
Software Tool Article metrics
Revised
InferAMP, a python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports
[version 3; peer review: 2 approved]
Paraic A. Kenny
Peer Reviewers Andrew C. Nelson; Oscar Krijgsman
  • Funder
  • Gundersen Medical Foundation
LATEST VERSION PUBLISHED 26 Sep 2019
https://doi.org/10.12688/f1000research.20233.1
Software Tool Article metrics
A Sequence Distance Graph framework for genome assembly and analysis
[version 1; peer review: 2 approved, 1 approved with reservations]
Luis Yanes, Gonzalo Garcia Accinelli, Jonathan Wright, Ben J. Ward, Bernardo J. Clavijo
Peer Reviewers Erik Garrison; Eric T. Dawson; Max Alekseyev and Pavel Avdeyev
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 23 Aug 2019
https://doi.org/10.12688/f1000research.19140.1
Software Tool Article metrics
Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich’s ataxia, and other rare iron-related diseases
[version 1; peer review: 2 approved]
Gloria C. Ferreira, Jenna Oberstaller, Renée Fonseca, Thomas E. Keller, Swamy Rakesh Adapa, Justin Gibbons, Chengqi Wang, Xiaoming Liu, Chang Li, Minh Pham, Guy W. Dayhoff II, Linh M. Duong, Luis Tañón Reyes, Luciano Enrique Laratelli, Douglas Franz, Segun Fatumo, ATM Golam Bari, Audrey Freischel, Lindsey Fiedler, Omkar Dokur, Krishna Sharma, Deborah Cragun, Ben Busby, Rays H.Y. Jiang
Peer Reviewers Karl E Anderson; Robert J. Desnick
  • Funders
  • American Cancer Society
  • WHC
  • U.S. National Library of Medicine
  • University of South Florida
  • National Science Foundation
PUBLISHED 19 Jul 2019
https://doi.org/10.12688/f1000research.18674.2
Software Tool Article metrics
Revised
CGAT-core: a python framework for building scalable, reproducible computational biology workflows
[version 2; peer review: 1 approved, 1 approved with reservations]
Adam P. Cribbs, Sebastian Luna-Valero, Charlotte George, Ian M. Sudbery, Antonio J. Berlanga-Taylor, Stephen N. Sansom, Tom Smith, Nicholas E. Ilott, Jethro Johnson, Jakub Scaber, Katherine Brown, David Sims, Andreas Heger
Peer Reviewers Devon P. Ryan; Alexander Peltzer
  • Funder
  • Medical Research Council
LATEST VERSION PUBLISHED 16 Jul 2019
https://doi.org/10.12688/f1000research.19675.1
Software Tool Article metrics
Large-scale sequence comparisons with sourmash
[version 1; peer review: 2 approved]
N. Tessa Pierce, Luiz Irber, Taylor Reiter, Phillip Brooks, C. Titus Brown
Peer Reviewers Brad Solomon; Rayan Chikhi
  • Funders
  • Gordon and Betty Moore Foundation
  • National Science Foundation
PUBLISHED 04 Jul 2019
https://doi.org/10.12688/f1000research.16483.2
Software Tool Article metrics
Revised
FDTool: a Python application to mine for functional dependencies and candidate keys in tabular data
[version 2; peer review: 2 approved]
Matt Buranosky, Elmar Stellnberger, Emily Pfaff, David Diaz-Sanchez, Cavin Ward-Caviness
Peer Reviewers Howard J. Hamilton and Shubhashis Shil; Sayan Mukherjee
  • Funder
  • U.S. Environmental Protection Agency
LATEST VERSION PUBLISHED 19 Jun 2019
https://doi.org/10.12688/f1000research.18952.1
Software Tool Article metrics
Detection and mitigation of spurious antisense expression with RoSA
[version 1; peer review: 2 approved with reservations]
Kira Mourão, Nicholas J. Schurch, Radek Lucoszek, Kimon Froussios, Katarzyna MacKinnon, Céline Duc, Gordon Simpson, Geoffrey J. Barton
Peer Reviewers Ian Sudbery; John Casement and Andreas Werner
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 07 Jun 2019
https://doi.org/10.12688/f1000research.18187.1
Method Article metrics
FaceSync: Open source framework for recording facial expressions with head-mounted cameras
[version 1; peer review: 2 approved]
Jin Hyun Cheong, Sawyer Brooks, Luke J. Chang
Peer Reviewers Elliott Ross; Sylwia Hyniewska
PUBLISHED 21 May 2019
https://doi.org/10.12688/f1000research.18676.1
Software Tool Article metrics
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
[version 1; peer review: 2 approved]
Saket Choudhary
Peer Reviewers Simon Andrews; Ryan K. Dale
PUBLISHED 23 Apr 2019
https://doi.org/10.12688/f1000research.18458.2
Software Tool Article metrics
Revised
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
[version 2; peer review: 2 approved]
Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Peer Reviewers Marta Szachniuk; Jerome Waldispühl and Roman Sarrazin-Gendron
  • Funder
  • Austrian Science Fund
LATEST VERSION PUBLISHED 23 Apr 2019
https://doi.org/10.12688/f1000research.17548.2
Software Tool Article metrics
Revised
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
[version 2; peer review: 2 approved]
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Peer Reviewers Bastian Greshake Tzovaras and Ngoc-Vinh Tran; Laurent Gatto
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • University College London
  • Swiss State Secretariat for Education
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 29 Mar 2019
https://doi.org/10.12688/f1000research.17456.1
Software Tool Article metrics
pdb-tools: a swiss army knife for molecular structures
[version 1; peer review: 2 approved]
João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
Peer Reviewers Bruno L. Victor; Peter W. Rose
  • Funders
  • Niels-Stensen Fellowship
  • Horizon 2020
PUBLISHED 20 Dec 2018
21-40 of 47 ARTICLES
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