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https://doi.org/10.12688/f1000research.26872.2
Software Tool Article metrics
Revised
Fiji plugins for qualitative image annotations: routine analysis and application to image classification
[version 2; peer review: 2 approved, 1 approved with reservations]
Laurent S. V. Thomas, Franz Schaefer, Jochen Gehrig
Peer Reviewers Jan Eglinger; Christian Tischer and Aliaksandr Halavatyi; Elisabet Teixido
  • Funder
  • Horizon 2020
LATEST VERSION PUBLISHED 12 Feb 2021
https://doi.org/10.12688/f1000research.51312.1
Study Protocol metrics
Guidance for ensuring fair and ethical broad consent for future use. A scoping review protocol.
[version 1; peer review: 2 approved]
Lauren Maxwell, Regina Gilyan, Sayali Arvind Chavan, Laura Merson, Abha Saxena, Rob Terry
Peer Reviewers David Osrin; Limbanazo Matandika
  • Funder
  • World Health Organization
PUBLISHED 11 Feb 2021
https://doi.org/10.12688/f1000research.26848.2
Software Tool Article metrics
Revised
CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline
[version 2; peer review: 2 approved]
Dustin B. Miller, Stephen R. Piccolo
Peer Reviewers Soohyun Lee; Sushant Patil
LATEST VERSION PUBLISHED 10 Feb 2021
https://doi.org/10.12688/f1000research.27112.2
Software Tool Article metrics
Revised
MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy
[version 2; peer review: 2 approved]
Sébastien Tosi, Lídia Bardia, Maria Jose Barallobre, Arrate Muñoz-Barrutia, María Luisa Soto-Montenegro, Julien Colombelli
Peer Reviewers Stephan Preibisch; Francesco Pampaloni
  • Funders
  • Instituto de Salud Carlos III
  • Ministerio de Ciencia, Innovación y Universidades
  • Ministerio de Economía y Competitividad
  • European Regional Development Fund
LATEST VERSION PUBLISHED 04 Feb 2021
https://doi.org/10.12688/f1000research.29988.1
Data Note metrics
rt-me-fMRI: a task and resting state dataset for real-time, multi-echo fMRI methods development and validation
[version 1; peer review: 1 approved, 1 approved with reservations]
Stephan Heunis, Marcel Breeuwer, César Caballero-Gaudes, Lydia Hellrung, Willem Huijbers, Jacobus F.A. Jansen, Rolf Lamerichs, Svitlana Zinger, Albert P. Aldenkamp
Peer Reviewers Klaus Mathiak; Christian Paret
  • Funders
  • Spanish Ministry of Science, Innovation and Universities
  • Philips Research
  • Horizon 2020
  • Health-Holland
  • Spanish Ministry of Economy and Competitiveness
  • Basque Government
PUBLISHED 04 Feb 2021
https://doi.org/10.12688/f1000research.27621.1
Data Note metrics
A studyforrest extension, an annotation of spoken language in the German dubbed movie “Forrest Gump” and its audio-description
[version 1; peer review: 1 approved, 2 approved with reservations]
Christian Olaf Häusler, Michael Hanke
Peer Reviewers Giada Lettieri; Martin Wegrzyn; Roberta Rocca
  • Funders
  • Bundesministerium für Bildung und Forschung
  • German federal state of Saxony-Anhalt
  • European Regional Development Fund
  • National Science Foundation
PUBLISHED 28 Jan 2021
https://doi.org/10.12688/f1000research.23224.2
Opinion Article metrics
Revised
An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
[version 2; peer review: 2 approved]
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bader, Lutz Brusch, Christian Busse, Gerasimos Chourdakis, Piotr Wojciech Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernadette Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Jan Hegewald, Sibylle Hermann, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H.C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Joerg Schaarschmidt, Heidi Seibold, Jan P. Thiele, Benjamin Uekermann, Stefan Unger, Rudolf Weeber
Peer Reviewers Wilhelm Hasselbring; Radovan Bast
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Karlsruher Institut für Technologie
LATEST VERSION PUBLISHED 26 Jan 2021
https://doi.org/10.12688/f1000research.26429.2
Software Tool Article metrics
Revised
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
[version 2; peer review: 2 approved]
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Peer Reviewers Kim-Anh Lê Cao; Anais Baudot, Judith Lambert and Laurent Tichit
  • Funders
  • Villum Fonden
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.28288.1
Research Article metrics
Comparison of different machine learning methods and dimensionality reduction for classification astrocytoma and glioblastoma tissues by mass spectra
[version 1; peer review: 1 approved with reservations, 1 not approved]
Evgeny S. Zhvansky, Anatoly A. Sorokin, Denis S. Zavorotnyuk, Vsevolod A. Shurkhay, Vasiliy A. Eliferov, Denis S. Bormotov, Daniil G. Ivanov, Alexander A. Potapov
Peer Reviewers Sergei A. Moshkovskii; Konstantin Chingin
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 21 Jan 2021
https://doi.org/10.12688/f1000research.28224.1
Software Tool Article metrics
The Paramak: automated parametric geometry construction for fusion reactor designs.
[version 1; peer review: 2 approved]
Jonathan Shimwell, John Billingsley, Rémi Delaporte-Mathurin, Declan Morbey, Matthew Bluteau, Patrick Shriwise, Andrew Davis
Peer Reviewers Yuefeng Qiu; Jingang Liang
  • Funders
  • RCUK Energy Programme
  • EPSRC
PUBLISHED 18 Jan 2021
https://doi.org/10.12688/f1000research.23378.3
Research Article metrics
Revised
Pictures over words: a cross-sectional study reporting short term memory abilities in children
[version 3; peer review: 2 approved]
Aysha Rooha, Malavika Anakkathil Anil, Jayashree S. Bhat
Peer Reviewers Ramesh Kaipa; Raju Sapkota
LATEST VERSION PUBLISHED 08 Jan 2021
https://doi.org/10.12688/f1000research.26880.2
Software Tool Article metrics
Revised
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME
[version 2; peer review: 3 approved]
Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Gokhan Goy, Rehman Qureshi, Louise C. Showe
Peer Reviewers Marco Chierici; Osman Ugur Sezerman; Abhishek Kumar
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 05 Jan 2021
https://doi.org/10.12688/f1000research.27019.2
Software Tool Article metrics
Revised
Automated cell tracking using StarDist and TrackMate
[version 2; peer review: 3 approved]
Elnaz Fazeli, Nathan H. Roy, Gautier Follain, Romain F. Laine, Lucas von Chamier, Pekka E. Hänninen, John E. Eriksson, Jean-Yves Tinevez, Guillaume Jacquemet
Peer Reviewers Lachlan W. Whitehead; Ignacio Arganda-Carreras; Vinay Swaminathan
  • Funders
  • Academy of Finland
  • National Cancer Center Finland
  • American Institute for Cancer Research
  • Sigrid Juselius Foundation
  • Medical Research Council
  • Åbo Akademi University Research Foundation
  • National Institutes of Health
  • Cancer Research Institute
LATEST VERSION PUBLISHED 21 Dec 2020
https://doi.org/10.12688/f1000research.26459.1
Software Tool Article metrics PEER REVIEW DISCONTINUED
Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences
[version 1; peer review: 1 approved with reservations]
Jenna Oberstaller, Swamy Rakesh Adapa, Guy W. Dayhoff II, Justin Gibbons, Thomas E. Keller, Chang Li, Jean Lim, Minh Pham, Anujit Sarkar, Ravi Sharma, Agaz H. Wani, Andrea Vianello, Linh M. Duong, Chenggi Wang, Celine Grace F. Atkinson, Madeleine Barrow, Nathan W. Van Bibber, Jan Dahrendorff, David A. E. Dean, Omkar Dokur, Gloria C. Ferreira, Mitchell Hastings, Gregory S. Herbert, Khandaker Tasnim Huq, Youngchul Kim, Xiangyun Liao, XiaoMing Liu, Fahad Mansuri, Lynn B. Martin, Elizabeth M. Miller, Ojas Natarajan, Jinyong Pang, Francesca Prieto, Peter W. Radulovic, Vyoma Sheth, Matthew Sumpter, Desirae Sutherland, Nisha Vijayakumar, Rays H. Y. Jiang
Peer Reviewers Sucheta Tripathy
  • Funder
  • University of South Florida
PUBLISHED 17 Dec 2020
https://doi.org/10.12688/f1000research.26923.2
Research Article metrics
Revised
Cross-sectional study of Facebook addiction in a sample of Nepalese population
[version 2; peer review: 2 approved]
Alok Atreya, Samata Nepal, Prakash Thapa
Peer Reviewers Kishor Adhikari; Abhishek Das
LATEST VERSION PUBLISHED 04 Dec 2020
https://doi.org/10.12688/f1000research.27188.1
Software Tool Article metrics
isa4j: a scalable Java library for creating ISA-Tab metadata
[version 1; peer review: 2 approved]
Dennis Psaroudakis, Feng Liu, Patrick König, Uwe Scholz, Astrid Junker, Matthias Lange, Daniel Arend
Peer Reviewers Massimiliano Izzo; Nils Hoffmann
  • Funders
  • ELIXIR
  • German Ministry of Education and Research (BMBF)
PUBLISHED 03 Dec 2020
https://doi.org/10.12688/f1000research.27179.1
Software Tool Article metrics
Semi-automated analysis of dot blots using ImageJ/Fiji
[version 1; peer review: 2 approved with reservations]
Anna H. Klemm
Peer Reviewers Christopher Schmied; Bram van den Broek
  • Funders
  • Ludwig Maximilian University of Munich
  • SciLifeLab
PUBLISHED 01 Dec 2020
https://doi.org/10.12688/f1000research.24956.2
Software Tool Article metrics
Revised
gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
[version 2; peer review: 2 approved]
Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Peer Reviewers Egon L. Willighagen; Ewy Mathe
  • Funders
  • Eesti Teadusagentuur
  • Seventh Framework Programme
  • European Regional Development Fund
LATEST VERSION PUBLISHED 17 Nov 2020
https://doi.org/10.12688/f1000research.23214.2
Software Tool Article metrics
Revised
CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets
[version 2; peer review: 2 approved, 1 not approved]
Sandeep Kasaragod, Varshasnata Mohanty, Ankur Tyagi, Santosh Kumar Behera, Arun H. Patil, Sneha M. Pinto, T. S. Keshava Prasad, Prashant Kumar Modi, Harsha Gowda
Peer Reviewers Suresh Mathivanan; Richard Kumaran Kandasamy; Jorge Duitama and Daniel Mahecha
  • Funders
  • Indian Council of Medical Research
  • Department of Science and Technology, Ministry of Science and Technology, India
  • Department of Biotechnology, Ministry of Science and Technology, India
LATEST VERSION PUBLISHED 16 Nov 2020
https://doi.org/10.12688/f1000research.15666.3
Research Article metrics
Revised
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
[version 3; peer review: 2 approved]
Angelo Duò, Mark D. Robinson, Charlotte Soneson
Peer Reviewers Jean Fan; Saskia Freytag
  • Funders
  • Swiss National Science Foundation
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 16 Nov 2020
361-380 of 1,016 ARTICLES
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